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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: 6-127475402-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=127475402&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MTCL3",
"hgnc_id": 21494,
"hgvs_c": "c.2624A>C",
"hgvs_p": "p.Asn875Thr",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_001400265.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000255330",
"hgnc_id": null,
"hgvs_c": "n.2624A>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000481848.6",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "SOGA3-KIAA0408",
"hgnc_id": null,
"hgvs_c": "n.3469A>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "NR_174482.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.6488,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "6",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.703295111656189,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 947,
"aa_ref": "N",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3996,
"cdna_start": 3469,
"cds_end": null,
"cds_length": 2844,
"cds_start": 2624,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001400265.1",
"gene_hgnc_id": 21494,
"gene_symbol": "MTCL3",
"hgvs_c": "c.2624A>C",
"hgvs_p": "p.Asn875Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000525778.6",
"protein_coding": true,
"protein_id": "NP_001387194.1",
"strand": false,
"transcript": "NM_001400265.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 947,
"aa_ref": "N",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3996,
"cdna_start": 3469,
"cds_end": null,
"cds_length": 2844,
"cds_start": 2624,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000525778.6",
"gene_hgnc_id": 21494,
"gene_symbol": "MTCL3",
"hgvs_c": "c.2624A>C",
"hgvs_p": "p.Asn875Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001400265.1",
"protein_coding": true,
"protein_id": "ENSP00000434570.1",
"strand": false,
"transcript": "ENST00000525778.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 11464,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000481848.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255330",
"hgvs_c": "n.2624A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000455908.1",
"strand": false,
"transcript": "ENST00000481848.6",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 944,
"aa_ref": "N",
"aa_start": 875,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3711,
"cdna_start": 3025,
"cds_end": null,
"cds_length": 2835,
"cds_start": 2624,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000465909.3",
"gene_hgnc_id": 21494,
"gene_symbol": "MTCL3",
"hgvs_c": "c.2624A>C",
"hgvs_p": "p.Asn875Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435559.1",
"strand": false,
"transcript": "ENST00000465909.3",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 761,
"aa_ref": "N",
"aa_start": 692,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2881,
"cdna_start": 2077,
"cds_end": null,
"cds_length": 2286,
"cds_start": 2075,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000703793.1",
"gene_hgnc_id": 21494,
"gene_symbol": "MTCL3",
"hgvs_c": "c.2075A>C",
"hgvs_p": "p.Asn692Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000515479.1",
"strand": false,
"transcript": "ENST00000703793.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 900,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000464495.4",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255330",
"hgvs_c": "n.71A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456668.2",
"strand": false,
"transcript": "ENST00000464495.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3350,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000473298.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255330",
"hgvs_c": "n.662A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000456172.1",
"strand": false,
"transcript": "ENST00000473298.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 772,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000474293.2",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000255330",
"hgvs_c": "n.293A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000474293.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 11834,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NR_174482.1",
"gene_hgnc_id": null,
"gene_symbol": "SOGA3-KIAA0408",
"hgvs_c": "n.3469A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_174482.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs750180009",
"effect": "missense_variant",
"frequency_reference_population": 6.8447207e-7,
"gene_hgnc_id": 21494,
"gene_symbol": "MTCL3",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84472e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.966,
"pos": 127475402,
"ref": "T",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.416,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001400265.1"
}
]
}