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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: 5-127440835-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=127440835&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 127440835,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000503335.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His",
"transcript": "NM_001256545.2",
"protein_id": "NP_001243474.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2330,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2609,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "ENST00000503335.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His",
"transcript": "ENST00000503335.7",
"protein_id": "ENSP00000423354.2",
"transcript_support_level": 1,
"aa_start": 777,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2330,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2609,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "NM_001256545.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His",
"transcript": "ENST00000274473.6",
"protein_id": "ENSP00000274473.6",
"transcript_support_level": 1,
"aa_start": 777,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2330,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2597,
"cdna_end": null,
"cdna_length": 7594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His",
"transcript": "NM_032446.3",
"protein_id": "NP_115822.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2330,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2660,
"cdna_end": null,
"cdna_length": 7657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2495G>A",
"hgvs_p": "p.Arg832His",
"transcript": "XM_017009987.2",
"protein_id": "XP_016865476.1",
"transcript_support_level": null,
"aa_start": 832,
"aa_end": null,
"aa_length": 1195,
"cds_start": 2495,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 3156,
"cdna_end": null,
"cdna_length": 8153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His",
"transcript": "XM_011543694.1",
"protein_id": "XP_011541996.1",
"transcript_support_level": null,
"aa_start": 777,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2330,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2404,
"cdna_end": null,
"cdna_length": 7401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.1190G>A",
"hgvs_p": "p.Arg397His",
"transcript": "XM_017009988.2",
"protein_id": "XP_016865477.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 760,
"cds_start": 1190,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 5591,
"cdna_end": null,
"cdna_length": 10588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "n.571G>A",
"hgvs_p": null,
"transcript": "ENST00000506709.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"dbsnp": "rs565304206",
"frequency_reference_population": 0.000056997567,
"hom_count_reference_population": 0,
"allele_count_reference_population": 92,
"gnomad_exomes_af": 0.0000540436,
"gnomad_genomes_af": 0.0000853455,
"gnomad_exomes_ac": 79,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6128237843513489,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.487,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2691,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1_Supporting",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000503335.7",
"gene_symbol": "MEGF10",
"hgnc_id": 29634,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2330G>A",
"hgvs_p": "p.Arg777His"
}
],
"clinvar_disease": "MEGF10-related myopathy,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4 O:1",
"phenotype_combined": "MEGF10-related myopathy|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}