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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: 21-43743730-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=43743730&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 43743730,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003681.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "NM_003681.5",
"protein_id": "NP_003672.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 312,
"cds_start": 254,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000291565.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003681.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "ENST00000291565.9",
"protein_id": "ENSP00000291565.4",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 312,
"cds_start": 254,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003681.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000291565.9"
},
{
"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": 3,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.247+1959C>T",
"hgvs_p": null,
"transcript": "ENST00000468090.5",
"protein_id": "ENSP00000418359.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 284,
"cds_start": null,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000468090.5"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "n.224C>T",
"hgvs_p": null,
"transcript": "ENST00000343528.10",
"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": "ENST00000343528.10"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "ENST00000867731.1",
"protein_id": "ENSP00000537790.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 371,
"cds_start": 254,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867731.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "ENST00000941196.1",
"protein_id": "ENSP00000611255.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 352,
"cds_start": 254,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941196.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "ENST00000867732.1",
"protein_id": "ENSP00000537791.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 335,
"cds_start": 254,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867732.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met",
"transcript": "ENST00000933237.1",
"protein_id": "ENSP00000603296.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 329,
"cds_start": 254,
"cds_end": null,
"cds_length": 990,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933237.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.149C>T",
"hgvs_p": "p.Thr50Met",
"transcript": "ENST00000867733.1",
"protein_id": "ENSP00000537792.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 277,
"cds_start": 149,
"cds_end": null,
"cds_length": 834,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867733.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Thr45Met",
"transcript": "NM_001331030.2",
"protein_id": "NP_001317959.1",
"transcript_support_level": null,
"aa_start": 45,
"aa_end": null,
"aa_length": 272,
"cds_start": 134,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001331030.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.134C>T",
"hgvs_p": "p.Thr45Met",
"transcript": "ENST00000467908.1",
"protein_id": "ENSP00000420708.1",
"transcript_support_level": 3,
"aa_start": 45,
"aa_end": null,
"aa_length": 272,
"cds_start": 134,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000467908.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.536C>T",
"hgvs_p": "p.Thr179Met",
"transcript": "XM_005261195.3",
"protein_id": "XP_005261252.2",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 406,
"cds_start": 536,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261195.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.437C>T",
"hgvs_p": "p.Thr146Met",
"transcript": "XM_047441001.1",
"protein_id": "XP_047296957.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 373,
"cds_start": 437,
"cds_end": null,
"cds_length": 1122,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441001.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.281C>T",
"hgvs_p": "p.Thr94Met",
"transcript": "XM_005261196.4",
"protein_id": "XP_005261253.1",
"transcript_support_level": null,
"aa_start": 94,
"aa_end": null,
"aa_length": 321,
"cds_start": 281,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261196.4"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.80C>T",
"hgvs_p": "p.Thr27Met",
"transcript": "XM_047441002.1",
"protein_id": "XP_047296958.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 254,
"cds_start": 80,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441002.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.80C>T",
"hgvs_p": "p.Thr27Met",
"transcript": "XM_047441003.1",
"protein_id": "XP_047296959.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 254,
"cds_start": 80,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441003.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.35C>T",
"hgvs_p": "p.Thr12Met",
"transcript": "XM_005261199.3",
"protein_id": "XP_005261256.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 239,
"cds_start": 35,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005261199.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.35C>T",
"hgvs_p": "p.Thr12Met",
"transcript": "XM_011529761.2",
"protein_id": "XP_011528063.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 239,
"cds_start": 35,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011529761.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.35C>T",
"hgvs_p": "p.Thr12Met",
"transcript": "XM_047441004.1",
"protein_id": "XP_047296960.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 239,
"cds_start": 35,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441004.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.35C>T",
"hgvs_p": "p.Thr12Met",
"transcript": "XM_047441005.1",
"protein_id": "XP_047296961.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 239,
"cds_start": 35,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441005.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.35C>T",
"hgvs_p": "p.Thr12Met",
"transcript": "XM_047441006.1",
"protein_id": "XP_047296962.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 239,
"cds_start": 35,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441006.1"
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"hgvs_c": "c.143-2349C>T",
"hgvs_p": null,
"transcript": "ENST00000933238.1",
"protein_id": "ENSP00000603297.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 249,
"cds_start": null,
"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": "ENST00000933238.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
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"biotype": "pseudogene",
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{
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"biotype": "pseudogene",
"feature": "ENST00000398085.7"
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
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"exon_count": 5,
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"biotype": "pseudogene",
"feature": "ENST00000470029.5"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
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"gene_symbol": "PDXK",
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{
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"protein_coding": false,
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"non_coding_transcript_exon_variant"
],
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{
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"non_coding_transcript_exon_variant"
],
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"gene_symbol": "PDXK",
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"transcript": "ENST00000490666.5",
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"feature": "ENST00000490666.5"
},
{
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"consequences": [
"non_coding_transcript_exon_variant"
],
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"gene_symbol": "PDXK",
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"transcript": "ENST00000498040.5",
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"biotype": "pseudogene",
"feature": "ENST00000498040.5"
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],
"gene_symbol": "PDXK",
"gene_hgnc_id": 8819,
"dbsnp": "rs149442489",
"frequency_reference_population": 0.000082577,
"hom_count_reference_population": 0,
"allele_count_reference_population": 133,
"gnomad_exomes_af": 0.0000788458,
"gnomad_genomes_af": 0.000118363,
"gnomad_exomes_ac": 115,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.36479243636131287,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.332,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1592,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.055,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
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"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_003681.5",
"gene_symbol": "PDXK",
"hgnc_id": 8819,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.254C>T",
"hgvs_p": "p.Thr85Met"
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],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}