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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: 19-42297251-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=42297251&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 42297251,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002573.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "NM_002573.4",
"protein_id": "NP_002564.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262890.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002573.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "ENST00000262890.8",
"protein_id": "ENSP00000262890.2",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002573.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262890.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "NM_001145939.2",
"protein_id": "NP_001139411.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145939.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "NM_001145940.1",
"protein_id": "NP_001139412.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001145940.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "ENST00000538771.5",
"protein_id": "ENSP00000444935.1",
"transcript_support_level": 2,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000538771.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn",
"transcript": "ENST00000877854.1",
"protein_id": "ENSP00000547913.1",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 231,
"cds_start": 523,
"cds_end": null,
"cds_length": 696,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877854.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Asp173Asn",
"transcript": "ENST00000916656.1",
"protein_id": "ENSP00000586715.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 229,
"cds_start": 517,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916656.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Asp162Asn",
"transcript": "ENST00000877855.1",
"protein_id": "ENSP00000547914.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 218,
"cds_start": 484,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877855.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.457G>A",
"hgvs_p": "p.Asp153Asn",
"transcript": "ENST00000916659.1",
"protein_id": "ENSP00000586718.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 209,
"cds_start": 457,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916659.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.433G>A",
"hgvs_p": "p.Asp145Asn",
"transcript": "ENST00000594989.5",
"protein_id": "ENSP00000471933.1",
"transcript_support_level": 5,
"aa_start": 145,
"aa_end": null,
"aa_length": 201,
"cds_start": 433,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000594989.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.406G>A",
"hgvs_p": "p.Asp136Asn",
"transcript": "ENST00000916658.1",
"protein_id": "ENSP00000586717.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 192,
"cds_start": 406,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916658.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Asp134Asn",
"transcript": "ENST00000916662.1",
"protein_id": "ENSP00000586721.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 190,
"cds_start": 400,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916662.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.385G>A",
"hgvs_p": "p.Asp129Asn",
"transcript": "ENST00000916661.1",
"protein_id": "ENSP00000586720.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 185,
"cds_start": 385,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916661.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Asp123Asn",
"transcript": "ENST00000916657.1",
"protein_id": "ENSP00000586716.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 179,
"cds_start": 367,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916657.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Asp112Asn",
"transcript": "ENST00000916660.1",
"protein_id": "ENSP00000586719.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 168,
"cds_start": 334,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916660.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.283G>A",
"hgvs_p": "p.Asp95Asn",
"transcript": "ENST00000877856.1",
"protein_id": "ENSP00000547915.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 151,
"cds_start": 283,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877856.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Asp162Asn",
"transcript": "XM_017026846.2",
"protein_id": "XP_016882335.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 218,
"cds_start": 484,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026846.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Asp162Asn",
"transcript": "XM_017026847.2",
"protein_id": "XP_016882336.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 218,
"cds_start": 484,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026847.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Asp162Asn",
"transcript": "XM_017026848.1",
"protein_id": "XP_016882337.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 218,
"cds_start": 484,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026848.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.*29G>A",
"hgvs_p": null,
"transcript": "ENST00000595530.5",
"protein_id": "ENSP00000473065.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": null,
"cds_end": null,
"cds_length": 494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000595530.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"hgvs_c": "c.*65G>A",
"hgvs_p": null,
"transcript": "ENST00000596265.5",
"protein_id": "ENSP00000470753.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 138,
"cds_start": null,
"cds_end": null,
"cds_length": 419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596265.5"
}
],
"gene_symbol": "PAFAH1B3",
"gene_hgnc_id": 8576,
"dbsnp": "rs766373467",
"frequency_reference_population": 0.00006009973,
"hom_count_reference_population": 0,
"allele_count_reference_population": 97,
"gnomad_exomes_af": 0.0000513065,
"gnomad_genomes_af": 0.000144564,
"gnomad_exomes_ac": 75,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1929798424243927,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.14,
"revel_prediction": "Benign",
"alphamissense_score": 0.4639,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.112,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_002573.4",
"gene_symbol": "PAFAH1B3",
"hgnc_id": 8576,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.523G>A",
"hgvs_p": "p.Asp175Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}