← 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: 4-87977065-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=87977065&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 87977065,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001040058.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "NM_001040058.2",
"protein_id": "NP_001035147.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 314,
"cds_start": 61,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000395080.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040058.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000395080.8",
"protein_id": "ENSP00000378517.3",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 314,
"cds_start": 61,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001040058.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395080.8"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000237623.11",
"protein_id": "ENSP00000237623.7",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 300,
"cds_start": 61,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000237623.11"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000360804.4",
"protein_id": "ENSP00000354042.4",
"transcript_support_level": 1,
"aa_start": 21,
"aa_end": null,
"aa_length": 287,
"cds_start": 61,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360804.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.159C>A",
"hgvs_p": null,
"transcript": "ENST00000508002.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000508002.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.161C>A",
"hgvs_p": null,
"transcript": "ENST00000509659.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000509659.5"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000614857.5",
"protein_id": "ENSP00000477824.2",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 314,
"cds_start": 61,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614857.5"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000882523.1",
"protein_id": "ENSP00000552582.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 314,
"cds_start": 61,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882523.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000942419.1",
"protein_id": "ENSP00000612478.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 314,
"cds_start": 61,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942419.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "NM_000582.3",
"protein_id": "NP_000573.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 300,
"cds_start": 61,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000582.3"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000942420.1",
"protein_id": "ENSP00000612479.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 300,
"cds_start": 61,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942420.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000920430.1",
"protein_id": "ENSP00000590489.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 295,
"cds_start": 61,
"cds_end": null,
"cds_length": 888,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920430.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "NM_001040060.2",
"protein_id": "NP_001035149.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 287,
"cds_start": 61,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040060.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000882524.1",
"protein_id": "ENSP00000552583.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 287,
"cds_start": 61,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882524.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "NM_001251829.2",
"protein_id": "NP_001238758.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 273,
"cds_start": 61,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001251829.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000508233.6",
"protein_id": "ENSP00000422973.2",
"transcript_support_level": 2,
"aa_start": 21,
"aa_end": null,
"aa_length": 273,
"cds_start": 61,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508233.6"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys",
"transcript": "ENST00000682655.1",
"protein_id": "ENSP00000508280.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 192,
"cds_start": 61,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682655.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.-90C>A",
"hgvs_p": null,
"transcript": "NM_001251830.2",
"protein_id": "NP_001238759.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 327,
"cds_start": null,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001251830.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.55-3C>A",
"hgvs_p": null,
"transcript": "ENST00000882522.1",
"protein_id": "ENSP00000552581.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 311,
"cds_start": null,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882522.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "c.55-3C>A",
"hgvs_p": null,
"transcript": "ENST00000882525.1",
"protein_id": "ENSP00000552584.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 297,
"cds_start": null,
"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": "ENST00000882525.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.162C>A",
"hgvs_p": null,
"transcript": "ENST00000504310.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000504310.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.77C>A",
"hgvs_p": null,
"transcript": "ENST00000505146.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000505146.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.162C>A",
"hgvs_p": null,
"transcript": "ENST00000509334.5",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000509334.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.162C>A",
"hgvs_p": null,
"transcript": "ENST00000513981.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000513981.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.162C>A",
"hgvs_p": null,
"transcript": "ENST00000681973.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000681973.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1243C>A",
"hgvs_p": null,
"transcript": "ENST00000682554.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000682554.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1243C>A",
"hgvs_p": null,
"transcript": "ENST00000682599.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000682599.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.62C>A",
"hgvs_p": null,
"transcript": "ENST00000682627.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000682627.1"
},
{
"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": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.468C>A",
"hgvs_p": null,
"transcript": "ENST00000682865.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000682865.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.117C>A",
"hgvs_p": null,
"transcript": "ENST00000683087.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000683087.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1263C>A",
"hgvs_p": null,
"transcript": "ENST00000683440.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000683440.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1243C>A",
"hgvs_p": null,
"transcript": "ENST00000683620.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000683620.1"
},
{
"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": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1352C>A",
"hgvs_p": null,
"transcript": "ENST00000684106.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000684106.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1243C>A",
"hgvs_p": null,
"transcript": "ENST00000684450.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000684450.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"hgvs_c": "n.1352C>A",
"hgvs_p": null,
"transcript": "ENST00000684710.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000684710.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286618",
"gene_hgnc_id": null,
"hgvs_c": "n.308-1203G>T",
"hgvs_p": null,
"transcript": "ENST00000662475.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000662475.1"
}
],
"gene_symbol": "SPP1",
"gene_hgnc_id": 11255,
"dbsnp": "rs141235817",
"frequency_reference_population": 0.00008179229,
"hom_count_reference_population": 0,
"allele_count_reference_population": 132,
"gnomad_exomes_af": 0.0000862037,
"gnomad_genomes_af": 0.0000394244,
"gnomad_exomes_ac": 126,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.059816956520080566,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.081,
"revel_prediction": "Benign",
"alphamissense_score": 0.0817,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.692,
"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_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001040058.2",
"gene_symbol": "SPP1",
"hgnc_id": 11255,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.61C>A",
"hgvs_p": "p.Gln21Lys"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000662475.1",
"gene_symbol": "ENSG00000286618",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.308-1203G>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}