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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-48909809-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48909809&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 48909809,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_001282651.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "NM_005660.3",
"protein_id": "NP_005651.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 396,
"cds_start": null,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000247138.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005660.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "ENST00000247138.11",
"protein_id": "ENSP00000247138.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 396,
"cds_start": null,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005660.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000247138.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "ENST00000376521.6",
"protein_id": "ENSP00000365704.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": null,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376521.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "ENST00000445167.7",
"protein_id": "ENSP00000402726.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": null,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000445167.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.358+5G>A",
"hgvs_p": null,
"transcript": "NM_001282651.2",
"protein_id": "NP_001269580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 421,
"cds_start": null,
"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": "NM_001282651.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.358+5G>A",
"hgvs_p": null,
"transcript": "ENST00000452555.7",
"protein_id": "ENSP00000416002.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 421,
"cds_start": null,
"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": "ENST00000452555.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.313+5G>A",
"hgvs_p": null,
"transcript": "ENST00000876225.1",
"protein_id": "ENSP00000546284.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 409,
"cds_start": null,
"cds_end": null,
"cds_length": 1230,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876225.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.313+5G>A",
"hgvs_p": null,
"transcript": "NM_001282650.2",
"protein_id": "NP_001269579.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 406,
"cds_start": null,
"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": "NM_001282650.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.313+5G>A",
"hgvs_p": null,
"transcript": "ENST00000616181.5",
"protein_id": "ENSP00000478617.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 406,
"cds_start": null,
"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": "ENST00000616181.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "NM_001042498.3",
"protein_id": "NP_001035963.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": null,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042498.3"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.91+1737G>A",
"hgvs_p": null,
"transcript": "NM_001282649.2",
"protein_id": "NP_001269578.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 332,
"cds_start": null,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282649.2"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.91+1737G>A",
"hgvs_p": null,
"transcript": "ENST00000635589.1",
"protein_id": "ENSP00000489197.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 332,
"cds_start": null,
"cds_end": null,
"cds_length": 999,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635589.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "NM_001032289.3",
"protein_id": "NP_001027460.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 242,
"cds_start": null,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001032289.3"
},
{
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"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "NM_001282647.2",
"protein_id": "NP_001269576.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282647.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.274+5G>A",
"hgvs_p": null,
"transcript": "ENST00000376529.8",
"protein_id": "ENSP00000365712.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 224,
"cds_start": null,
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"cds_length": 675,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376529.8"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.202+5G>A",
"hgvs_p": null,
"transcript": "NM_001282648.2",
"protein_id": "NP_001269577.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": null,
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"cds_length": 657,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001282648.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.202+5G>A",
"hgvs_p": null,
"transcript": "ENST00000376515.8",
"protein_id": "ENSP00000365698.3",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": null,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376515.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.58+5G>A",
"hgvs_p": null,
"transcript": "ENST00000413561.7",
"protein_id": "ENSP00000393233.3",
"transcript_support_level": 2,
"aa_start": null,
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"aa_length": 201,
"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000413561.7"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.235+44G>A",
"hgvs_p": null,
"transcript": "ENST00000635238.1",
"protein_id": "ENSP00000489515.1",
"transcript_support_level": 3,
"aa_start": null,
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"aa_length": 190,
"cds_start": null,
"cds_end": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635238.1"
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.313+5G>A",
"hgvs_p": null,
"transcript": "ENST00000635015.1",
"protein_id": "ENSP00000489089.1",
"transcript_support_level": 2,
"aa_start": null,
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"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000635015.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.58+5G>A",
"hgvs_p": null,
"transcript": "ENST00000446885.1",
"protein_id": "ENSP00000415518.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": null,
"cds_end": null,
"cds_length": 527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446885.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC35A2",
"gene_hgnc_id": 11022,
"hgvs_c": "c.271+5G>A",
"hgvs_p": null,
"transcript": "ENST00000635460.1",
"protein_id": "ENSP00000489339.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": null,
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{
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{
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{
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{
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{
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"transcript": "ENST00000635628.1",
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"biotype": "nonsense_mediated_decay",
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],
"gene_symbol": "SLC35A2",
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"dbsnp": "rs1060503677",
"frequency_reference_population": 0.000016648242,
"hom_count_reference_population": 6,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000174585,
"gnomad_genomes_af": 0.00000884682,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 1,
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"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.75,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9539999961853027,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.75,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.604,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.58,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999930861344917,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 5,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001282651.2",
"gene_symbol": "SLC35A2",
"hgnc_id": 11022,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "XL,Unknown",
"hgvs_c": "c.358+5G>A",
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}
],
"clinvar_disease": "SLC35A2-congenital disorder of glycosylation,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "SLC35A2-congenital disorder of glycosylation|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}