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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: 17-17506246-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=17506246&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 17506246,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000255389.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Val212Met",
"transcript": "NM_148172.3",
"protein_id": "NP_680477.1",
"transcript_support_level": null,
"aa_start": 212,
"aa_end": null,
"aa_length": 236,
"cds_start": 634,
"cds_end": null,
"cds_length": 711,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1021,
"mane_select": "ENST00000255389.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Val212Met",
"transcript": "ENST00000255389.10",
"protein_id": "ENSP00000255389.5",
"transcript_support_level": 1,
"aa_start": 212,
"aa_end": null,
"aa_length": 236,
"cds_start": 634,
"cds_end": null,
"cds_length": 711,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 1021,
"mane_select": "NM_148172.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Val175Met",
"transcript": "ENST00000395782.5",
"protein_id": "ENSP00000379128.1",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 199,
"cds_start": 523,
"cds_end": null,
"cds_length": 600,
"cdna_start": 590,
"cdna_end": null,
"cdna_length": 895,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Val175Met",
"transcript": "ENST00000395783.5",
"protein_id": "ENSP00000379129.1",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 199,
"cds_start": 523,
"cds_end": null,
"cds_length": 600,
"cdna_start": 703,
"cdna_end": null,
"cdna_length": 1008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.665G>A",
"hgvs_p": "p.Ser222Asn",
"transcript": "NM_001267552.2",
"protein_id": "NP_001254481.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 232,
"cds_start": 665,
"cds_end": null,
"cds_length": 699,
"cdna_start": 747,
"cdna_end": null,
"cdna_length": 1052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.665G>A",
"hgvs_p": "p.Ser222Asn",
"transcript": "ENST00000395781.6",
"protein_id": "ENSP00000379127.2",
"transcript_support_level": 2,
"aa_start": 222,
"aa_end": null,
"aa_length": 232,
"cds_start": 665,
"cds_end": null,
"cds_length": 699,
"cdna_start": 747,
"cdna_end": null,
"cdna_length": 1050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.568G>A",
"hgvs_p": "p.Val190Met",
"transcript": "NM_001267551.2",
"protein_id": "NP_001254480.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 214,
"cds_start": 568,
"cds_end": null,
"cds_length": 645,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.602G>A",
"hgvs_p": "p.Ser201Asn",
"transcript": "ENST00000435340.6",
"protein_id": "ENSP00000391288.2",
"transcript_support_level": 5,
"aa_start": 201,
"aa_end": null,
"aa_length": 211,
"cds_start": 602,
"cds_end": null,
"cds_length": 636,
"cdna_start": 655,
"cdna_end": null,
"cdna_length": 960,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Val175Met",
"transcript": "NM_007169.3",
"protein_id": "NP_009100.2",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 199,
"cds_start": 523,
"cds_end": null,
"cds_length": 600,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 1023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Val175Met",
"transcript": "NM_148173.2",
"protein_id": "NP_680478.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 199,
"cds_start": 523,
"cds_end": null,
"cds_length": 600,
"cdna_start": 621,
"cdna_end": null,
"cdna_length": 926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.649G>A",
"hgvs_p": "p.Val217Met",
"transcript": "XM_006721418.5",
"protein_id": "XP_006721481.3",
"transcript_support_level": null,
"aa_start": 217,
"aa_end": null,
"aa_length": 241,
"cds_start": 649,
"cds_end": null,
"cds_length": 726,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 1233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Val175Met",
"transcript": "XM_024450532.2",
"protein_id": "XP_024306300.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 199,
"cds_start": 523,
"cds_end": null,
"cds_length": 600,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 1019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Val101Met",
"transcript": "XM_017024016.2",
"protein_id": "XP_016879505.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 125,
"cds_start": 301,
"cds_end": null,
"cds_length": 378,
"cdna_start": 498,
"cdna_end": null,
"cdna_length": 803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.128G>A",
"hgvs_p": null,
"transcript": "ENST00000477595.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.498G>A",
"hgvs_p": null,
"transcript": "ENST00000484838.6",
"protein_id": null,
"transcript_support_level": 2,
"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": 803,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.368G>A",
"hgvs_p": null,
"transcript": "ENST00000490392.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.*132G>A",
"hgvs_p": null,
"transcript": "ENST00000580147.5",
"protein_id": "ENSP00000463112.1",
"transcript_support_level": 3,
"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": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.78G>A",
"hgvs_p": null,
"transcript": "ENST00000582268.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 383,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"hgvs_c": "n.*132G>A",
"hgvs_p": null,
"transcript": "ENST00000580147.5",
"protein_id": "ENSP00000463112.1",
"transcript_support_level": 3,
"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": 708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286430",
"gene_hgnc_id": null,
"hgvs_c": "n.120+2122C>T",
"hgvs_p": null,
"transcript": "ENST00000671231.1",
"protein_id": null,
"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": 820,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PEMT",
"gene_hgnc_id": 8830,
"dbsnp": "rs7946",
"frequency_reference_population": 0.68627167,
"hom_count_reference_population": 385160,
"allele_count_reference_population": 1082411,
"gnomad_exomes_af": 0.696531,
"gnomad_genomes_af": 0.590187,
"gnomad_exomes_ac": 992607,
"gnomad_genomes_ac": 89804,
"gnomad_exomes_homalt": 356567,
"gnomad_genomes_homalt": 28593,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000022130116121843457,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.069,
"revel_prediction": "Benign",
"alphamissense_score": 0.1241,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.091,
"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,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000255389.10",
"gene_symbol": "PEMT",
"hgnc_id": 8830,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.634G>A",
"hgvs_p": "p.Val212Met"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000671231.1",
"gene_symbol": "ENSG00000286430",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.120+2122C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}