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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: 8-43122726-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=43122726&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 43122726,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000331373.10",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"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.902T>C",
"hgvs_p": "p.Met301Thr",
"transcript": "NM_032237.5",
"protein_id": "NP_115613.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 350,
"cds_start": 902,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1160,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": "ENST00000331373.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.902T>C",
"hgvs_p": "p.Met301Thr",
"transcript": "ENST00000331373.10",
"protein_id": "ENSP00000331258.5",
"transcript_support_level": 2,
"aa_start": 301,
"aa_end": null,
"aa_length": 350,
"cds_start": 902,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1160,
"cdna_end": null,
"cdna_length": 1868,
"mane_select": "NM_032237.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.902T>C",
"hgvs_p": "p.Met301Thr",
"transcript": "NM_001277971.2",
"protein_id": "NP_001264900.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 350,
"cds_start": 902,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1064,
"cdna_end": null,
"cdna_length": 1772,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.902T>C",
"hgvs_p": "p.Met301Thr",
"transcript": "ENST00000676193.1",
"protein_id": "ENSP00000502774.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 350,
"cds_start": 902,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1081,
"cdna_end": null,
"cdna_length": 9535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.860T>C",
"hgvs_p": "p.Met287Thr",
"transcript": "ENST00000674937.1",
"protein_id": "ENSP00000501823.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 336,
"cds_start": 860,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 3922,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.620T>C",
"hgvs_p": "p.Met207Thr",
"transcript": "ENST00000674676.1",
"protein_id": "ENSP00000502544.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 256,
"cds_start": 620,
"cds_end": null,
"cds_length": 771,
"cdna_start": 620,
"cdna_end": null,
"cdna_length": 1951,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"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.620T>C",
"hgvs_p": "p.Met207Thr",
"transcript": "ENST00000675675.1",
"protein_id": "ENSP00000501793.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 256,
"cds_start": 620,
"cds_end": null,
"cds_length": 771,
"cdna_start": 620,
"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.*698T>C",
"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.620T>C",
"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.*822T>C",
"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.620T>C",
"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.*687T>C",
"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.*698T>C",
"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.*822T>C",
"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.*687T>C",
"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": "rs33920561",
"frequency_reference_population": 0.0003091322,
"hom_count_reference_population": 2,
"allele_count_reference_population": 499,
"gnomad_exomes_af": 0.00016554,
"gnomad_genomes_af": 0.00168735,
"gnomad_exomes_ac": 242,
"gnomad_genomes_ac": 257,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.009953051805496216,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.109,
"revel_prediction": "Benign",
"alphamissense_score": 0.2915,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.86,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000331373.10",
"gene_symbol": "POMK",
"hgnc_id": 26267,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.902T>C",
"hgvs_p": "p.Met301Thr"
}
],
"clinvar_disease": " 12, type a,Limb-girdle muscular dystrophy due to POMK deficiency,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12;Limb-girdle muscular dystrophy due to POMK deficiency|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}