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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: 8-43122830-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=43122830&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 43122830,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000331373.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"transcript": "NM_032237.5",
"protein_id": "NP_115613.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 350,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": "ENST00000331373.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"transcript": "ENST00000331373.10",
"protein_id": "ENSP00000331258.5",
"transcript_support_level": 2,
"aa_start": 336,
"aa_end": null,
"aa_length": 350,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1264,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": "NM_032237.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"transcript": "NM_001277971.2",
"protein_id": "NP_001264900.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 350,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1168,
"cdna_end": null,
"cdna_length": 1772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn",
"transcript": "ENST00000676193.1",
"protein_id": "ENSP00000502774.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 350,
"cds_start": 1006,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1185,
"cdna_end": null,
"cdna_length": 9535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.964G>A",
"hgvs_p": "p.Asp322Asn",
"transcript": "ENST00000674937.1",
"protein_id": "ENSP00000501823.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 336,
"cds_start": 964,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 3922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.724G>A",
"hgvs_p": "p.Asp242Asn",
"transcript": "ENST00000674676.1",
"protein_id": "ENSP00000502544.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 256,
"cds_start": 724,
"cds_end": null,
"cds_length": 771,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 1951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "c.724G>A",
"hgvs_p": "p.Asp242Asn",
"transcript": "ENST00000675675.1",
"protein_id": "ENSP00000501793.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 256,
"cds_start": 724,
"cds_end": null,
"cds_length": 771,
"cdna_start": 724,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*802G>A",
"hgvs_p": null,
"transcript": "ENST00000614426.2",
"protein_id": "ENSP00000478821.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.724G>A",
"hgvs_p": null,
"transcript": "ENST00000674646.1",
"protein_id": "ENSP00000501703.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3576,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*926G>A",
"hgvs_p": null,
"transcript": "ENST00000674782.1",
"protein_id": "ENSP00000501683.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.724G>A",
"hgvs_p": null,
"transcript": "ENST00000675322.1",
"protein_id": "ENSP00000502235.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*791G>A",
"hgvs_p": null,
"transcript": "ENST00000676178.1",
"protein_id": "ENSP00000502007.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*802G>A",
"hgvs_p": null,
"transcript": "ENST00000614426.2",
"protein_id": "ENSP00000478821.2",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*926G>A",
"hgvs_p": null,
"transcript": "ENST00000674782.1",
"protein_id": "ENSP00000501683.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"hgvs_c": "n.*791G>A",
"hgvs_p": null,
"transcript": "ENST00000676178.1",
"protein_id": "ENSP00000502007.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "POMK",
"gene_hgnc_id": 26267,
"dbsnp": "rs113361507",
"frequency_reference_population": 0.00093937095,
"hom_count_reference_population": 18,
"allele_count_reference_population": 1516,
"gnomad_exomes_af": 0.000775182,
"gnomad_genomes_af": 0.00251553,
"gnomad_exomes_ac": 1133,
"gnomad_genomes_ac": 383,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003647923469543457,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.013,
"revel_prediction": "Benign",
"alphamissense_score": 0.0611,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.966,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000331373.10",
"gene_symbol": "POMK",
"hgnc_id": 26267,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1006G>A",
"hgvs_p": "p.Asp336Asn"
}
],
"clinvar_disease": " 12, type a,Limb-girdle muscular dystrophy due to POMK deficiency,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),POMK-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12;Limb-girdle muscular dystrophy due to POMK deficiency|not provided|POMK-related disorder|not specified",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}