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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: 14-49789166-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=49789166&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 49789166,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004713.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2875G>A",
"hgvs_p": "p.Asp959Asn",
"transcript": "NM_004713.6",
"protein_id": "NP_004704.3",
"transcript_support_level": null,
"aa_start": 959,
"aa_end": null,
"aa_length": 1076,
"cds_start": 2875,
"cds_end": null,
"cds_length": 3231,
"cdna_start": 2910,
"cdna_end": null,
"cdna_length": 5819,
"mane_select": "ENST00000298310.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004713.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2875G>A",
"hgvs_p": "p.Asp959Asn",
"transcript": "ENST00000298310.10",
"protein_id": "ENSP00000298310.5",
"transcript_support_level": 5,
"aa_start": 959,
"aa_end": null,
"aa_length": 1076,
"cds_start": 2875,
"cds_end": null,
"cds_length": 3231,
"cdna_start": 2910,
"cdna_end": null,
"cdna_length": 5819,
"mane_select": "NM_004713.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298310.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "n.1699G>A",
"hgvs_p": null,
"transcript": "ENST00000556074.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000556074.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2872G>A",
"hgvs_p": "p.Asp958Asn",
"transcript": "ENST00000925604.1",
"protein_id": "ENSP00000595663.1",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 1075,
"cds_start": 2872,
"cds_end": null,
"cds_length": 3228,
"cdna_start": 2907,
"cdna_end": null,
"cdna_length": 4081,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925604.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2839G>A",
"hgvs_p": "p.Asp947Asn",
"transcript": "ENST00000925603.1",
"protein_id": "ENSP00000595662.1",
"transcript_support_level": null,
"aa_start": 947,
"aa_end": null,
"aa_length": 1064,
"cds_start": 2839,
"cds_end": null,
"cds_length": 3195,
"cdna_start": 2904,
"cdna_end": null,
"cdna_length": 4082,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925603.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2812G>A",
"hgvs_p": "p.Asp938Asn",
"transcript": "NM_001301732.3",
"protein_id": "NP_001288661.2",
"transcript_support_level": null,
"aa_start": 938,
"aa_end": null,
"aa_length": 1055,
"cds_start": 2812,
"cds_end": null,
"cds_length": 3168,
"cdna_start": 2847,
"cdna_end": null,
"cdna_length": 5756,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001301732.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2788G>A",
"hgvs_p": "p.Asp930Asn",
"transcript": "ENST00000943722.1",
"protein_id": "ENSP00000613781.1",
"transcript_support_level": null,
"aa_start": 930,
"aa_end": null,
"aa_length": 1047,
"cds_start": 2788,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 2857,
"cdna_end": null,
"cdna_length": 4036,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943722.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2749G>A",
"hgvs_p": "p.Asp917Asn",
"transcript": "ENST00000555970.5",
"protein_id": "ENSP00000452540.1",
"transcript_support_level": 2,
"aa_start": 917,
"aa_end": null,
"aa_length": 997,
"cds_start": 2749,
"cds_end": null,
"cds_length": 2996,
"cdna_start": 2782,
"cdna_end": null,
"cdna_length": 3029,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555970.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2875G>A",
"hgvs_p": "p.Asp959Asn",
"transcript": "XM_047431911.1",
"protein_id": "XP_047287867.1",
"transcript_support_level": null,
"aa_start": 959,
"aa_end": null,
"aa_length": 993,
"cds_start": 2875,
"cds_end": null,
"cds_length": 2982,
"cdna_start": 2910,
"cdna_end": null,
"cdna_length": 3096,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431911.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Asp730Asn",
"transcript": "XM_017021761.2",
"protein_id": "XP_016877250.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 847,
"cds_start": 2188,
"cds_end": null,
"cds_length": 2544,
"cdna_start": 3007,
"cdna_end": null,
"cdna_length": 5916,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017021761.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "c.2188G>A",
"hgvs_p": "p.Asp730Asn",
"transcript": "XM_047431912.1",
"protein_id": "XP_047287868.1",
"transcript_support_level": null,
"aa_start": 730,
"aa_end": null,
"aa_length": 847,
"cds_start": 2188,
"cds_end": null,
"cds_length": 2544,
"cdna_start": 2300,
"cdna_end": null,
"cdna_length": 5209,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431912.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "n.884G>A",
"hgvs_p": null,
"transcript": "ENST00000556691.5",
"protein_id": null,
"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": 2062,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000556691.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"hgvs_c": "n.2364G>A",
"hgvs_p": null,
"transcript": "ENST00000556925.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 3699,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000556925.5"
}
],
"gene_symbol": "NEMF",
"gene_hgnc_id": 10663,
"dbsnp": "rs376310576",
"frequency_reference_population": 0.000033461853,
"hom_count_reference_population": 0,
"allele_count_reference_population": 54,
"gnomad_exomes_af": 0.0000342056,
"gnomad_genomes_af": 0.0000263109,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1868305206298828,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.056,
"revel_prediction": "Benign",
"alphamissense_score": 0.0852,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.806,
"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": 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_004713.6",
"gene_symbol": "NEMF",
"hgnc_id": 10663,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2875G>A",
"hgvs_p": "p.Asp959Asn"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}