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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: 3-125451397-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=125451397&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 125451397,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003794.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1213G>A",
"hgvs_p": "p.Ala405Thr",
"transcript": "NM_003794.4",
"protein_id": "NP_003785.1",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 450,
"cds_start": 1213,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000251775.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003794.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1213G>A",
"hgvs_p": "p.Ala405Thr",
"transcript": "ENST00000251775.9",
"protein_id": "ENSP00000251775.4",
"transcript_support_level": 1,
"aa_start": 405,
"aa_end": null,
"aa_length": 450,
"cds_start": 1213,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003794.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000251775.9"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1336G>A",
"hgvs_p": "p.Ala446Thr",
"transcript": "ENST00000873377.1",
"protein_id": "ENSP00000543436.1",
"transcript_support_level": null,
"aa_start": 446,
"aa_end": null,
"aa_length": 491,
"cds_start": 1336,
"cds_end": null,
"cds_length": 1476,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873377.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1330G>A",
"hgvs_p": "p.Ala444Thr",
"transcript": "ENST00000873378.1",
"protein_id": "ENSP00000543437.1",
"transcript_support_level": null,
"aa_start": 444,
"aa_end": null,
"aa_length": 489,
"cds_start": 1330,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873378.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1309G>A",
"hgvs_p": "p.Ala437Thr",
"transcript": "ENST00000873370.1",
"protein_id": "ENSP00000543429.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 482,
"cds_start": 1309,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873370.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1252G>A",
"hgvs_p": "p.Ala418Thr",
"transcript": "ENST00000873374.1",
"protein_id": "ENSP00000543433.1",
"transcript_support_level": null,
"aa_start": 418,
"aa_end": null,
"aa_length": 463,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1392,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873374.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1234G>A",
"hgvs_p": "p.Ala412Thr",
"transcript": "ENST00000873372.1",
"protein_id": "ENSP00000543431.1",
"transcript_support_level": null,
"aa_start": 412,
"aa_end": null,
"aa_length": 457,
"cds_start": 1234,
"cds_end": null,
"cds_length": 1374,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873372.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1201G>A",
"hgvs_p": "p.Ala401Thr",
"transcript": "ENST00000945406.1",
"protein_id": "ENSP00000615465.1",
"transcript_support_level": null,
"aa_start": 401,
"aa_end": null,
"aa_length": 446,
"cds_start": 1201,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945406.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1186G>A",
"hgvs_p": "p.Ala396Thr",
"transcript": "ENST00000873373.1",
"protein_id": "ENSP00000543432.1",
"transcript_support_level": null,
"aa_start": 396,
"aa_end": null,
"aa_length": 441,
"cds_start": 1186,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873373.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1147G>A",
"hgvs_p": "p.Ala383Thr",
"transcript": "ENST00000873375.1",
"protein_id": "ENSP00000543434.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 428,
"cds_start": 1147,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873375.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1123G>A",
"hgvs_p": "p.Ala375Thr",
"transcript": "ENST00000945404.1",
"protein_id": "ENSP00000615463.1",
"transcript_support_level": null,
"aa_start": 375,
"aa_end": null,
"aa_length": 420,
"cds_start": 1123,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945404.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1084G>A",
"hgvs_p": "p.Ala362Thr",
"transcript": "ENST00000873371.1",
"protein_id": "ENSP00000543430.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 407,
"cds_start": 1084,
"cds_end": null,
"cds_length": 1224,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873371.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1078G>A",
"hgvs_p": "p.Ala360Thr",
"transcript": "ENST00000873376.1",
"protein_id": "ENSP00000543435.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 405,
"cds_start": 1078,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873376.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Ala253Thr",
"transcript": "ENST00000945405.1",
"protein_id": "ENSP00000615464.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 298,
"cds_start": 757,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000945405.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "c.1309G>A",
"hgvs_p": "p.Ala437Thr",
"transcript": "XM_017007414.3",
"protein_id": "XP_016862903.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 482,
"cds_start": 1309,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007414.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.*941G>A",
"hgvs_p": null,
"transcript": "ENST00000471751.5",
"protein_id": "ENSP00000420526.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471751.5"
},
{
"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": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.300G>A",
"hgvs_p": null,
"transcript": "ENST00000482965.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000482965.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.1121G>A",
"hgvs_p": null,
"transcript": "NR_073435.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_073435.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"hgvs_c": "n.*941G>A",
"hgvs_p": null,
"transcript": "ENST00000471751.5",
"protein_id": "ENSP00000420526.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471751.5"
}
],
"gene_symbol": "SNX4",
"gene_hgnc_id": 11175,
"dbsnp": "rs754873266",
"frequency_reference_population": 6.8450674e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84507e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11636537313461304,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.03,
"revel_prediction": "Benign",
"alphamissense_score": 0.0725,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.083,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_003794.4",
"gene_symbol": "SNX4",
"hgnc_id": 11175,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1213G>A",
"hgvs_p": "p.Ala405Thr"
}
],
"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
}