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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: X-48459000-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48459000&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 48459000,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_033518.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "NM_033518.4",
"protein_id": "NP_277053.2",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000620913.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033518.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000620913.5",
"protein_id": "ENSP00000481291.1",
"transcript_support_level": 5,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033518.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620913.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000595796.5",
"protein_id": "ENSP00000471683.1",
"transcript_support_level": 1,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595796.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1454T>C",
"hgvs_p": "p.Met485Thr",
"transcript": "ENST00000955855.1",
"protein_id": "ENSP00000625914.1",
"transcript_support_level": null,
"aa_start": 485,
"aa_end": null,
"aa_length": 506,
"cds_start": 1454,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955855.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1454T>C",
"hgvs_p": "p.Met485Thr",
"transcript": "ENST00000955856.1",
"protein_id": "ENSP00000625915.1",
"transcript_support_level": null,
"aa_start": 485,
"aa_end": null,
"aa_length": 506,
"cds_start": 1454,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955856.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875418.1",
"protein_id": "ENSP00000545477.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875418.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875419.1",
"protein_id": "ENSP00000545478.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875419.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875420.1",
"protein_id": "ENSP00000545479.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875420.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875421.1",
"protein_id": "ENSP00000545480.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875421.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875422.1",
"protein_id": "ENSP00000545481.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875422.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000875423.1",
"protein_id": "ENSP00000545482.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875423.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "ENST00000925238.1",
"protein_id": "ENSP00000595297.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925238.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1259T>C",
"hgvs_p": "p.Met420Thr",
"transcript": "ENST00000925234.1",
"protein_id": "ENSP00000595293.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 441,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925234.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1259T>C",
"hgvs_p": "p.Met420Thr",
"transcript": "ENST00000925239.1",
"protein_id": "ENSP00000595298.1",
"transcript_support_level": null,
"aa_start": 420,
"aa_end": null,
"aa_length": 441,
"cds_start": 1259,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925239.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1199T>C",
"hgvs_p": "p.Met400Thr",
"transcript": "ENST00000619100.4",
"protein_id": "ENSP00000478807.1",
"transcript_support_level": 2,
"aa_start": 400,
"aa_end": null,
"aa_length": 421,
"cds_start": 1199,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000619100.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1196T>C",
"hgvs_p": "p.Met399Thr",
"transcript": "ENST00000925235.1",
"protein_id": "ENSP00000595294.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 420,
"cds_start": 1196,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925235.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1106T>C",
"hgvs_p": "p.Met369Thr",
"transcript": "ENST00000925237.1",
"protein_id": "ENSP00000595296.1",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 390,
"cds_start": 1106,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925237.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1064T>C",
"hgvs_p": "p.Met355Thr",
"transcript": "ENST00000925236.1",
"protein_id": "ENSP00000595295.1",
"transcript_support_level": null,
"aa_start": 355,
"aa_end": null,
"aa_length": 376,
"cds_start": 1064,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925236.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1493T>C",
"hgvs_p": "p.Met498Thr",
"transcript": "XM_005272695.5",
"protein_id": "XP_005272752.3",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 519,
"cds_start": 1493,
"cds_end": null,
"cds_length": 1560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005272695.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1370T>C",
"hgvs_p": "p.Met457Thr",
"transcript": "XM_017029960.2",
"protein_id": "XP_016885449.1",
"transcript_support_level": null,
"aa_start": 457,
"aa_end": null,
"aa_length": 478,
"cds_start": 1370,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029960.2"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr",
"transcript": "XM_017029961.3",
"protein_id": "XP_016885450.1",
"transcript_support_level": null,
"aa_start": 451,
"aa_end": null,
"aa_length": 472,
"cds_start": 1352,
"cds_end": null,
"cds_length": 1419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029961.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"hgvs_c": "c.1459-236T>C",
"hgvs_p": null,
"transcript": "XM_005272694.4",
"protein_id": "XP_005272751.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 539,
"cds_start": null,
"cds_end": null,
"cds_length": 1620,
"cdna_start": null,
"cdna_end": null,
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{
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{
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"transcript": "XM_005272698.6",
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{
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"feature": "XM_006724569.4"
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{
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],
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{
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"gene_symbol": "SLC38A5",
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{
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"downstream_gene_variant"
],
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"gene_symbol": "SLC38A5",
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"biotype": "retained_intron",
"feature": "ENST00000480105.1"
}
],
"gene_symbol": "SLC38A5",
"gene_hgnc_id": 18070,
"dbsnp": "rs17281188",
"frequency_reference_population": 0.07683007,
"hom_count_reference_population": 32887,
"allele_count_reference_population": 91752,
"gnomad_exomes_af": 0.0769259,
"gnomad_genomes_af": 0.0759125,
"gnomad_exomes_ac": 83183,
"gnomad_genomes_ac": 8569,
"gnomad_exomes_homalt": 2287,
"gnomad_genomes_homalt": 277,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0017329752445220947,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.247,
"revel_prediction": "Benign",
"alphamissense_score": 0.4317,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.315,
"phylop100way_prediction": "Pathogenic",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_033518.4",
"gene_symbol": "SLC38A5",
"hgnc_id": 18070,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1352T>C",
"hgvs_p": "p.Met451Thr"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}