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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: 6-169710265-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=169710265&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PHF10",
"hgnc_id": 18250,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_018288.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 37,
"alphamissense_prediction": null,
"alphamissense_score": 0.0714,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.31,
"chr": "6",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.040585994720458984,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 498,
"aa_ref": "V",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2167,
"cdna_start": 1653,
"cds_end": null,
"cds_length": 1497,
"cds_start": 1084,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_018288.4",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000339209.9",
"protein_coding": true,
"protein_id": "NP_060758.2",
"strand": false,
"transcript": "NM_018288.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 498,
"aa_ref": "V",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2167,
"cdna_start": 1653,
"cds_end": null,
"cds_length": 1497,
"cds_start": 1084,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000339209.9",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018288.4",
"protein_coding": true,
"protein_id": "ENSP00000341805.4",
"strand": false,
"transcript": "ENST00000339209.9",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 451,
"aa_ref": "V",
"aa_start": 315,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1651,
"cdna_start": 1143,
"cds_end": null,
"cds_length": 1356,
"cds_start": 943,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000621772.4",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.943G>A",
"hgvs_p": "p.Val315Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000484117.1",
"strand": false,
"transcript": "ENST00000621772.4",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 377,
"aa_ref": "V",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4395,
"cdna_start": 1158,
"cds_end": null,
"cds_length": 1134,
"cds_start": 1084,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000612128.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479515.1",
"strand": false,
"transcript": "ENST00000612128.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4285,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000480008.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "n.1048G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000480008.1",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 500,
"aa_ref": "V",
"aa_start": 364,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1675,
"cdna_start": 1163,
"cds_end": null,
"cds_length": 1503,
"cds_start": 1090,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000885654.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1090G>A",
"hgvs_p": "p.Val364Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555713.1",
"strand": false,
"transcript": "ENST00000885654.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 496,
"aa_ref": "V",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2161,
"cdna_start": 1647,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1078,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_133325.3",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1078G>A",
"hgvs_p": "p.Val360Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_579866.2",
"strand": false,
"transcript": "NM_133325.3",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 496,
"aa_ref": "V",
"aa_start": 360,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1589,
"cdna_start": 1078,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1078,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000366780.8",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1078G>A",
"hgvs_p": "p.Val360Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000355743.4",
"strand": false,
"transcript": "ENST00000366780.8",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 496,
"aa_ref": "V",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1620,
"cdna_start": 1113,
"cds_end": null,
"cds_length": 1491,
"cds_start": 1084,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000885655.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555714.1",
"strand": false,
"transcript": "ENST00000885655.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 493,
"aa_ref": "V",
"aa_start": 357,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1678,
"cdna_start": 1167,
"cds_end": null,
"cds_length": 1482,
"cds_start": 1069,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000965605.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1069G>A",
"hgvs_p": "p.Val357Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635664.1",
"strand": false,
"transcript": "ENST00000965605.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 470,
"aa_ref": "V",
"aa_start": 334,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1599,
"cdna_start": 1087,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1000,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000885653.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1000G>A",
"hgvs_p": "p.Val334Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000555712.1",
"strand": false,
"transcript": "ENST00000885653.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 435,
"aa_ref": "V",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1417,
"cdna_start": 1098,
"cds_end": null,
"cds_length": 1308,
"cds_start": 1084,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000965606.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Val362Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000635665.1",
"strand": false,
"transcript": "ENST00000965606.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 446,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1514,
"cdna_start": null,
"cds_end": null,
"cds_length": 1341,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000930217.1",
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"hgvs_c": "c.957+2121G>A",
"hgvs_p": null,
"intron_rank": 8,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000600276.1",
"strand": false,
"transcript": "ENST00000930217.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs34227712",
"effect": "missense_variant",
"frequency_reference_population": 0.0000229444,
"gene_hgnc_id": 18250,
"gene_symbol": "PHF10",
"gnomad_exomes_ac": 25,
"gnomad_exomes_af": 0.0000171189,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 12,
"gnomad_genomes_af": 0.0000788322,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.9,
"pos": 169710265,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.321,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05999999865889549,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.06,
"transcript": "NM_018288.4"
}
]
}