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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: 18-2656077-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=2656077&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 2656077,
"ref": "T",
"alt": "G",
"effect": "start_lost",
"transcript": "NM_015295.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_015295.3",
"protein_id": "NP_056110.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 2005,
"cds_start": 2,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "ENST00000320876.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000320876.11",
"protein_id": "ENSP00000326603.7",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 2005,
"cds_start": 2,
"cds_end": null,
"cds_length": 6018,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 8833,
"mane_select": "NM_015295.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000688342.1",
"protein_id": "ENSP00000508422.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1961,
"cds_start": 2,
"cds_end": null,
"cds_length": 5886,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 6488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011525642.2",
"protein_id": "XP_011523944.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 2067,
"cds_start": 2,
"cds_end": null,
"cds_length": 6204,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 8936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047437426.1",
"protein_id": "XP_047293382.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1827,
"cds_start": 2,
"cds_end": null,
"cds_length": 5484,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 5932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047437428.1",
"protein_id": "XP_047293384.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1450,
"cds_start": 2,
"cds_end": null,
"cds_length": 4353,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 4828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047437429.1",
"protein_id": "XP_047293385.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1316,
"cds_start": 2,
"cds_end": null,
"cds_length": 3951,
"cdna_start": 352,
"cdna_end": null,
"cdna_length": 4339,
"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": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.159T>G",
"hgvs_p": null,
"transcript": "ENST00000684915.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3534,
"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": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.352T>G",
"hgvs_p": null,
"transcript": "XR_001753172.2",
"protein_id": null,
"transcript_support_level": null,
"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": 9051,
"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": 1,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.352T>G",
"hgvs_p": null,
"transcript": "XR_007066135.1",
"protein_id": null,
"transcript_support_level": null,
"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": 5706,
"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": 1,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "n.352T>G",
"hgvs_p": null,
"transcript": "XR_935055.3",
"protein_id": null,
"transcript_support_level": null,
"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": 5720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"hgvs_c": "c.-307T>G",
"hgvs_p": null,
"transcript": "XM_047437427.1",
"protein_id": "XP_047293383.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1939,
"cds_start": -4,
"cds_end": null,
"cds_length": 5820,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000293256",
"gene_hgnc_id": null,
"hgvs_c": "n.-207A>C",
"hgvs_p": null,
"transcript": "ENST00000733457.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1245,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMCHD1",
"gene_hgnc_id": 29090,
"dbsnp": "rs1555622203",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9024350643157959,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.186,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.188,
"phylop100way_prediction": "Benign",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "NM_015295.3",
"gene_symbol": "SMCHD1",
"hgnc_id": 29090,
"effects": [
"start_lost"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000733457.1",
"gene_symbol": "ENSG00000293256",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-207A>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}