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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: 12-124954003-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=124954003&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "DHX37",
"hgnc_id": 17210,
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_032656.4",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000301157",
"hgnc_id": null,
"hgvs_c": "n.134-2151A>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000776681.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 975160,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.84,
"chr": "12",
"clinvar_classification": "Benign",
"clinvar_disease": "46,Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies,XY sex reversal 11,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8399999737739563,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1157,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4559,
"cdna_start": null,
"cds_end": null,
"cds_length": 3474,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 27,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_032656.4",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000308736.7",
"protein_coding": true,
"protein_id": "NP_116045.2",
"strand": false,
"transcript": "NM_032656.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1157,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4559,
"cdna_start": null,
"cds_end": null,
"cds_length": 3474,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 27,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000308736.7",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032656.4",
"protein_coding": true,
"protein_id": "ENSP00000311135.2",
"strand": false,
"transcript": "ENST00000308736.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 998,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4112,
"cdna_start": null,
"cds_end": null,
"cds_length": 2997,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000544745.2",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2048-7T>C",
"hgvs_p": null,
"intron_rank": 16,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000439009.2",
"strand": false,
"transcript": "ENST00000544745.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1126,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4468,
"cdna_start": null,
"cds_end": null,
"cds_length": 3381,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880032.1",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2486-7T>C",
"hgvs_p": null,
"intron_rank": 18,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550091.1",
"strand": false,
"transcript": "ENST00000880032.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1113,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4363,
"cdna_start": null,
"cds_end": null,
"cds_length": 3342,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000921756.1",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2447-7T>C",
"hgvs_p": null,
"intron_rank": 18,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000591815.1",
"strand": false,
"transcript": "ENST00000921756.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1003,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4092,
"cdna_start": null,
"cds_end": null,
"cds_length": 3012,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000880033.1",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2117-7T>C",
"hgvs_p": null,
"intron_rank": 17,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000550092.1",
"strand": false,
"transcript": "ENST00000880033.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1175,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3672,
"cdna_start": null,
"cds_end": null,
"cds_length": 3528,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005253590.4",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005253647.1",
"strand": false,
"transcript": "XM_005253590.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1009,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": null,
"cds_end": null,
"cds_length": 3030,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047429218.1",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047285174.1",
"strand": false,
"transcript": "XM_047429218.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 904,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2961,
"cdna_start": null,
"cds_end": null,
"cds_length": 2715,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011538598.3",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2579-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536900.1",
"strand": false,
"transcript": "XM_011538598.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 881,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2951,
"cdna_start": null,
"cds_end": null,
"cds_length": 2646,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 21,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011538600.3",
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"hgvs_c": "c.2569-7T>C",
"hgvs_p": null,
"intron_rank": 19,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011536902.1",
"strand": false,
"transcript": "XM_011538600.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 448,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000776681.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000301157",
"hgvs_c": "n.134-2151A>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000776681.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0000356722501786047,
"dbsnp": "rs4606565",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": 0.6044812,
"gene_hgnc_id": 17210,
"gene_symbol": "DHX37",
"gnomad_exomes_ac": 887119,
"gnomad_exomes_af": 0.607103,
"gnomad_exomes_homalt": 272992,
"gnomad_genomes_ac": 88041,
"gnomad_genomes_af": 0.57927,
"gnomad_genomes_homalt": 26328,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 299320,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "46,XY sex reversal 11|Neurodevelopmental disorder with brain anomalies and with or without vertebral or cardiac anomalies|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.164,
"pos": 124954003,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_032656.4"
}
]
}