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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: 5-127438491-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=127438491&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 127438491,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000503335.7",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His",
"transcript": "NM_001256545.2",
"protein_id": "NP_001243474.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2157,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2436,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "ENST00000503335.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His",
"transcript": "ENST00000503335.7",
"protein_id": "ENSP00000423354.2",
"transcript_support_level": 1,
"aa_start": 719,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2157,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2436,
"cdna_end": null,
"cdna_length": 7606,
"mane_select": "NM_001256545.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His",
"transcript": "ENST00000274473.6",
"protein_id": "ENSP00000274473.6",
"transcript_support_level": 1,
"aa_start": 719,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2157,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2424,
"cdna_end": null,
"cdna_length": 7594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His",
"transcript": "NM_032446.3",
"protein_id": "NP_115822.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2157,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2487,
"cdna_end": null,
"cdna_length": 7657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2322T>C",
"hgvs_p": "p.His774His",
"transcript": "XM_017009987.2",
"protein_id": "XP_016865476.1",
"transcript_support_level": null,
"aa_start": 774,
"aa_end": null,
"aa_length": 1195,
"cds_start": 2322,
"cds_end": null,
"cds_length": 3588,
"cdna_start": 2983,
"cdna_end": null,
"cdna_length": 8153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His",
"transcript": "XM_011543694.1",
"protein_id": "XP_011541996.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1140,
"cds_start": 2157,
"cds_end": null,
"cds_length": 3423,
"cdna_start": 2231,
"cdna_end": null,
"cdna_length": 7401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "c.1017T>C",
"hgvs_p": "p.His339His",
"transcript": "XM_017009988.2",
"protein_id": "XP_016865477.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 760,
"cds_start": 1017,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 5418,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MEGF10",
"gene_hgnc_id": 29634,
"hgvs_c": "n.398T>C",
"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": "rs374544972",
"frequency_reference_population": 0.000015489448,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.00000957691,
"gnomad_genomes_af": 0.0000722961,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5600000023841858,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.62,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BP7,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BP7",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000503335.7",
"gene_symbol": "MEGF10",
"hgnc_id": 29634,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2157T>C",
"hgvs_p": "p.His719His"
}
],
"clinvar_disease": "MEGF10-related myopathy,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not provided|MEGF10-related myopathy",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}