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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-72581044-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=72581044&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 72581044,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001431068.1",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3630C>T",
"hgvs_p": "p.Tyr1210Tyr",
"transcript": "NM_002637.4",
"protein_id": "NP_002628.2",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3630,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373542.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002637.4"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3630C>T",
"hgvs_p": "p.Tyr1210Tyr",
"transcript": "ENST00000373542.9",
"protein_id": "ENSP00000362643.4",
"transcript_support_level": 1,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3630,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002637.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373542.9"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3591C>T",
"hgvs_p": "p.Tyr1197Tyr",
"transcript": "ENST00000339490.7",
"protein_id": "ENSP00000342469.3",
"transcript_support_level": 1,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3591,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000339490.7"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3414C>T",
"hgvs_p": "p.Tyr1138Tyr",
"transcript": "ENST00000541944.5",
"protein_id": "ENSP00000441251.1",
"transcript_support_level": 1,
"aa_start": 1138,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3414,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541944.5"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3681C>T",
"hgvs_p": "p.Tyr1227Tyr",
"transcript": "NM_001431068.1",
"protein_id": "NP_001417997.1",
"transcript_support_level": null,
"aa_start": 1227,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3681,
"cds_end": null,
"cds_length": 3723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001431068.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3681C>T",
"hgvs_p": "p.Tyr1227Tyr",
"transcript": "ENST00000373539.3",
"protein_id": "ENSP00000362640.3",
"transcript_support_level": 5,
"aa_start": 1227,
"aa_end": null,
"aa_length": 1240,
"cds_start": 3681,
"cds_end": null,
"cds_length": 3723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373539.3"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3591C>T",
"hgvs_p": "p.Tyr1197Tyr",
"transcript": "NM_001122670.2",
"protein_id": "NP_001116142.1",
"transcript_support_level": null,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3591,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001122670.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3591C>T",
"hgvs_p": "p.Tyr1197Tyr",
"transcript": "NM_001440787.1",
"protein_id": "NP_001427716.1",
"transcript_support_level": null,
"aa_start": 1197,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3591,
"cds_end": null,
"cds_length": 3633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440787.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3510C>T",
"hgvs_p": "p.Tyr1170Tyr",
"transcript": "ENST00000958860.1",
"protein_id": "ENSP00000628919.1",
"transcript_support_level": null,
"aa_start": 1170,
"aa_end": null,
"aa_length": 1183,
"cds_start": 3510,
"cds_end": null,
"cds_length": 3552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958860.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3504C>T",
"hgvs_p": "p.Tyr1168Tyr",
"transcript": "ENST00000373545.7",
"protein_id": "ENSP00000362646.3",
"transcript_support_level": 5,
"aa_start": 1168,
"aa_end": null,
"aa_length": 1181,
"cds_start": 3504,
"cds_end": null,
"cds_length": 3546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373545.7"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3489C>T",
"hgvs_p": "p.Tyr1163Tyr",
"transcript": "ENST00000929439.1",
"protein_id": "ENSP00000599498.1",
"transcript_support_level": null,
"aa_start": 1163,
"aa_end": null,
"aa_length": 1176,
"cds_start": 3489,
"cds_end": null,
"cds_length": 3531,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929439.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3453C>T",
"hgvs_p": "p.Tyr1151Tyr",
"transcript": "ENST00000898176.1",
"protein_id": "ENSP00000568235.1",
"transcript_support_level": null,
"aa_start": 1151,
"aa_end": null,
"aa_length": 1164,
"cds_start": 3453,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898176.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3414C>T",
"hgvs_p": "p.Tyr1138Tyr",
"transcript": "NM_001172436.2",
"protein_id": "NP_001165907.1",
"transcript_support_level": null,
"aa_start": 1138,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3414,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001172436.2"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3414C>T",
"hgvs_p": "p.Tyr1138Tyr",
"transcript": "NM_001440788.1",
"protein_id": "NP_001427717.1",
"transcript_support_level": null,
"aa_start": 1138,
"aa_end": null,
"aa_length": 1151,
"cds_start": 3414,
"cds_end": null,
"cds_length": 3456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440788.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3390C>T",
"hgvs_p": "p.Tyr1130Tyr",
"transcript": "ENST00000898177.1",
"protein_id": "ENSP00000568236.1",
"transcript_support_level": null,
"aa_start": 1130,
"aa_end": null,
"aa_length": 1143,
"cds_start": 3390,
"cds_end": null,
"cds_length": 3432,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898177.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3372C>T",
"hgvs_p": "p.Tyr1124Tyr",
"transcript": "ENST00000958862.1",
"protein_id": "ENSP00000628921.1",
"transcript_support_level": null,
"aa_start": 1124,
"aa_end": null,
"aa_length": 1137,
"cds_start": 3372,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958862.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3345C>T",
"hgvs_p": "p.Tyr1115Tyr",
"transcript": "ENST00000929440.1",
"protein_id": "ENSP00000599499.1",
"transcript_support_level": null,
"aa_start": 1115,
"aa_end": null,
"aa_length": 1128,
"cds_start": 3345,
"cds_end": null,
"cds_length": 3387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929440.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3333C>T",
"hgvs_p": "p.Tyr1111Tyr",
"transcript": "ENST00000958859.1",
"protein_id": "ENSP00000628918.1",
"transcript_support_level": null,
"aa_start": 1111,
"aa_end": null,
"aa_length": 1124,
"cds_start": 3333,
"cds_end": null,
"cds_length": 3375,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958859.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3282C>T",
"hgvs_p": "p.Tyr1094Tyr",
"transcript": "ENST00000958861.1",
"protein_id": "ENSP00000628920.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1107,
"cds_start": 3282,
"cds_end": null,
"cds_length": 3324,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958861.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3243C>T",
"hgvs_p": "p.Tyr1081Tyr",
"transcript": "ENST00000958858.1",
"protein_id": "ENSP00000628917.1",
"transcript_support_level": null,
"aa_start": 1081,
"aa_end": null,
"aa_length": 1094,
"cds_start": 3243,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958858.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3630C>T",
"hgvs_p": "p.Tyr1210Tyr",
"transcript": "XM_047442160.1",
"protein_id": "XP_047298116.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1223,
"cds_start": 3630,
"cds_end": null,
"cds_length": 3672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442160.1"
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"hgvs_c": "c.3453C>T",
"hgvs_p": "p.Tyr1151Tyr",
"transcript": "XM_006724661.3",
"protein_id": "XP_006724724.1",
"transcript_support_level": null,
"aa_start": 1151,
"aa_end": null,
"aa_length": 1164,
"cds_start": 3453,
"cds_end": null,
"cds_length": 3495,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006724661.3"
}
],
"gene_symbol": "PHKA1",
"gene_hgnc_id": 8925,
"dbsnp": "rs372291401",
"frequency_reference_population": 0.000010749852,
"hom_count_reference_population": 3,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000637966,
"gnomad_genomes_af": 0.0000535322,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5699999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.016,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2_Supporting",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2_Supporting"
],
"verdict": "Benign",
"transcript": "NM_001431068.1",
"gene_symbol": "PHKA1",
"hgnc_id": 8925,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.3681C>T",
"hgvs_p": "p.Tyr1227Tyr"
}
],
"clinvar_disease": "Glycogen storage disease IXd",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Glycogen storage disease IXd",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}