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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: 9-127935769-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=127935769&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DPM2",
"hgnc_id": 3006,
"hgvs_c": "c.208T>A",
"hgvs_p": "p.Ser70Thr",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_003863.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000227218",
"hgnc_id": null,
"hgvs_c": "n.126-4638A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000727590.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0563,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"chr": "9",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.19223323464393616,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 84,
"aa_ref": "S",
"aa_start": 70,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 912,
"cdna_start": 242,
"cds_end": null,
"cds_length": 255,
"cds_start": 208,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_003863.4",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.208T>A",
"hgvs_p": "p.Ser70Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000314392.13",
"protein_coding": true,
"protein_id": "NP_003854.1",
"strand": false,
"transcript": "NM_003863.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 84,
"aa_ref": "S",
"aa_start": 70,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 912,
"cdna_start": 242,
"cds_end": null,
"cds_length": 255,
"cds_start": 208,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000314392.13",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.208T>A",
"hgvs_p": "p.Ser70Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003863.4",
"protein_coding": true,
"protein_id": "ENSP00000322181.8",
"strand": false,
"transcript": "ENST00000314392.13",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 928,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000470181.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "n.500T>A",
"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": "ENST00000470181.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1662,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000495270.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "n.992T>A",
"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": "ENST00000495270.1",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 110,
"aa_ref": "S",
"aa_start": 96,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 996,
"cdna_start": 317,
"cds_end": null,
"cds_length": 333,
"cds_start": 286,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000911994.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.286T>A",
"hgvs_p": "p.Ser96Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582053.1",
"strand": false,
"transcript": "ENST00000911994.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 80,
"aa_ref": "S",
"aa_start": 66,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 881,
"cdna_start": 212,
"cds_end": null,
"cds_length": 243,
"cds_start": 196,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000957588.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.196T>A",
"hgvs_p": "p.Ser66Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627647.1",
"strand": false,
"transcript": "ENST00000957588.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 78,
"aa_ref": "S",
"aa_start": 64,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 903,
"cdna_start": 231,
"cds_end": null,
"cds_length": 237,
"cds_start": 190,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000911993.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.190T>A",
"hgvs_p": "p.Ser64Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582052.1",
"strand": false,
"transcript": "ENST00000911993.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 73,
"aa_ref": "S",
"aa_start": 59,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 862,
"cdna_start": 193,
"cds_end": null,
"cds_length": 222,
"cds_start": 175,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000898430.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.175T>A",
"hgvs_p": "p.Ser59Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568489.1",
"strand": false,
"transcript": "ENST00000898430.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 54,
"aa_ref": "S",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 822,
"cdna_start": 152,
"cds_end": null,
"cds_length": 165,
"cds_start": 118,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001378437.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.118T>A",
"hgvs_p": "p.Ser40Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001365366.1",
"strand": false,
"transcript": "NM_001378437.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 54,
"aa_ref": "S",
"aa_start": 40,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 841,
"cdna_start": 164,
"cds_end": null,
"cds_length": 165,
"cds_start": 118,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000898429.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "c.118T>A",
"hgvs_p": "p.Ser40Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568488.1",
"strand": false,
"transcript": "ENST00000898429.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 744,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000473360.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "n.358T>A",
"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": "ENST00000473360.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1035,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NR_165631.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "n.365T>A",
"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_165631.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 719,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_165632.1",
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"hgvs_c": "n.49T>A",
"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_165632.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 564,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000592240.6",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.143+1124A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000592240.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 540,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000727590.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.126-4638A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000727590.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000727591.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.100-4638A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000727591.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 504,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000727592.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.63-4626A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000727592.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 519,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000727593.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.143+1124A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000727593.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 427,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000727594.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000227218",
"hgvs_c": "n.63+1201A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000727594.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs759597928",
"effect": "missense_variant",
"frequency_reference_population": 6.844955e-7,
"gene_hgnc_id": 3006,
"gene_symbol": "DPM2",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84495e-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": "Benign",
"phylop100way_score": 0.79,
"pos": 127935769,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.161,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003863.4"
}
]
}