← Back to variant description
GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 9-128940428-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=128940428&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 128940428,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001100876.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "NM_001100876.2",
"protein_id": "NP_001094346.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000372592.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001100876.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000372592.8",
"protein_id": "ENSP00000361673.3",
"transcript_support_level": 2,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001100876.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372592.8"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.454G>A",
"hgvs_p": "p.Val152Met",
"transcript": "ENST00000421063.6",
"protein_id": "ENSP00000409928.2",
"transcript_support_level": 1,
"aa_start": 152,
"aa_end": null,
"aa_length": 270,
"cds_start": 454,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421063.6"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.495G>A",
"hgvs_p": "p.Ala165Ala",
"transcript": "ENST00000308941.9",
"protein_id": "ENSP00000309515.5",
"transcript_support_level": 1,
"aa_start": 165,
"aa_end": null,
"aa_length": 297,
"cds_start": 495,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308941.9"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.547G>A",
"hgvs_p": "p.Val183Met",
"transcript": "ENST00000875821.1",
"protein_id": "ENSP00000545880.1",
"transcript_support_level": null,
"aa_start": 183,
"aa_end": null,
"aa_length": 301,
"cds_start": 547,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875821.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875820.1",
"protein_id": "ENSP00000545879.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 298,
"cds_start": 517,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875820.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875825.1",
"protein_id": "ENSP00000545884.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 298,
"cds_start": 517,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875825.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875823.1",
"protein_id": "ENSP00000545882.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875823.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875828.1",
"protein_id": "ENSP00000545887.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875828.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875831.1",
"protein_id": "ENSP00000545890.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875831.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875832.1",
"protein_id": "ENSP00000545891.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875832.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000970310.1",
"protein_id": "ENSP00000640369.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 291,
"cds_start": 517,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970310.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Val170Met",
"transcript": "ENST00000875818.1",
"protein_id": "ENSP00000545877.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 288,
"cds_start": 508,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875818.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Val170Met",
"transcript": "ENST00000970309.1",
"protein_id": "ENSP00000640368.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 288,
"cds_start": 508,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970309.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.472G>A",
"hgvs_p": "p.Val158Met",
"transcript": "ENST00000875829.1",
"protein_id": "ENSP00000545888.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 276,
"cds_start": 472,
"cds_end": null,
"cds_length": 831,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875829.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.454G>A",
"hgvs_p": "p.Val152Met",
"transcript": "NM_001100877.1",
"protein_id": "NP_001094347.1",
"transcript_support_level": null,
"aa_start": 152,
"aa_end": null,
"aa_length": 270,
"cds_start": 454,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001100877.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.454G>A",
"hgvs_p": "p.Val152Met",
"transcript": "ENST00000353176.9",
"protein_id": "ENSP00000340945.5",
"transcript_support_level": 5,
"aa_start": 152,
"aa_end": null,
"aa_length": 270,
"cds_start": 454,
"cds_end": null,
"cds_length": 813,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000353176.9"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000875824.1",
"protein_id": "ENSP00000545883.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 252,
"cds_start": 517,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875824.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000970308.1",
"protein_id": "ENSP00000640367.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 252,
"cds_start": 517,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970308.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Val170Met",
"transcript": "ENST00000875833.1",
"protein_id": "ENSP00000545892.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 249,
"cds_start": 508,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875833.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.376G>A",
"hgvs_p": "p.Val126Met",
"transcript": "ENST00000875827.1",
"protein_id": "ENSP00000545886.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 244,
"cds_start": 376,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875827.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Val120Met",
"transcript": "ENST00000875822.1",
"protein_id": "ENSP00000545881.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 238,
"cds_start": 358,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875822.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Val120Met",
"transcript": "ENST00000875819.1",
"protein_id": "ENSP00000545878.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 199,
"cds_start": 358,
"cds_end": null,
"cds_length": 600,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875819.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000426694.5",
"protein_id": "ENSP00000412377.1",
"transcript_support_level": 3,
"aa_start": 173,
"aa_end": null,
"aa_length": 176,
"cds_start": 517,
"cds_end": null,
"cds_length": 531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426694.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.495G>A",
"hgvs_p": "p.Ala165Ala",
"transcript": "NM_174933.4",
"protein_id": "NP_777593.2",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 297,
"cds_start": 495,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_174933.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.213G>A",
"hgvs_p": "p.Ala71Ala",
"transcript": "ENST00000442837.5",
"protein_id": "ENSP00000407232.1",
"transcript_support_level": 5,
"aa_start": 71,
"aa_end": null,
"aa_length": 164,
"cds_start": 213,
"cds_end": null,
"cds_length": 495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442837.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.90G>A",
"hgvs_p": "p.Ala30Ala",
"transcript": "ENST00000419872.1",
"protein_id": "ENSP00000399438.1",
"transcript_support_level": 3,
"aa_start": 30,
"aa_end": null,
"aa_length": 97,
"cds_start": 90,
"cds_end": null,
"cds_length": 294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419872.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.458-171G>A",
"hgvs_p": null,
"transcript": "ENST00000875826.1",
"protein_id": "ENSP00000545885.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 248,
"cds_start": null,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875826.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.395-171G>A",
"hgvs_p": null,
"transcript": "ENST00000916274.1",
"protein_id": "ENSP00000586333.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 227,
"cds_start": null,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916274.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.458-1017G>A",
"hgvs_p": null,
"transcript": "ENST00000970311.1",
"protein_id": "ENSP00000640370.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 209,
"cds_start": null,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970311.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.395-1017G>A",
"hgvs_p": null,
"transcript": "ENST00000875830.1",
"protein_id": "ENSP00000545889.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": null,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875830.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "c.395-1017G>A",
"hgvs_p": null,
"transcript": "ENST00000916273.1",
"protein_id": "ENSP00000586332.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": null,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916273.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "n.*200G>A",
"hgvs_p": null,
"transcript": "ENST00000412476.5",
"protein_id": "ENSP00000401991.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000412476.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "n.*368G>A",
"hgvs_p": null,
"transcript": "ENST00000424503.1",
"protein_id": "ENSP00000412738.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000424503.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "n.36G>A",
"hgvs_p": null,
"transcript": "ENST00000487504.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000487504.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "n.*200G>A",
"hgvs_p": null,
"transcript": "ENST00000412476.5",
"protein_id": "ENSP00000401991.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000412476.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"hgvs_c": "n.*368G>A",
"hgvs_p": null,
"transcript": "ENST00000424503.1",
"protein_id": "ENSP00000412738.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000424503.1"
}
],
"gene_symbol": "PHYHD1",
"gene_hgnc_id": 23396,
"dbsnp": "rs371562024",
"frequency_reference_population": 0.00005204222,
"hom_count_reference_population": 0,
"allele_count_reference_population": 84,
"gnomad_exomes_af": 0.0000540399,
"gnomad_genomes_af": 0.0000328532,
"gnomad_exomes_ac": 79,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12963023781776428,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.248,
"revel_prediction": "Benign",
"alphamissense_score": 0.117,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -5.899,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001100876.2",
"gene_symbol": "PHYHD1",
"hgnc_id": 23396,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}