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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: 12-105031790-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=105031790&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 105031790,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001034173.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2389G>A",
"hgvs_p": "p.Gly797Arg",
"transcript": "NM_001034173.4",
"protein_id": "NP_001029345.2",
"transcript_support_level": null,
"aa_start": 797,
"aa_end": null,
"aa_length": 923,
"cds_start": 2389,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258494.14",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001034173.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2389G>A",
"hgvs_p": "p.Gly797Arg",
"transcript": "ENST00000258494.14",
"protein_id": "ENSP00000258494.9",
"transcript_support_level": 1,
"aa_start": 797,
"aa_end": null,
"aa_length": 923,
"cds_start": 2389,
"cds_end": null,
"cds_length": 2772,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001034173.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258494.14"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2416G>A",
"hgvs_p": "p.Gly806Arg",
"transcript": "ENST00000652515.1",
"protein_id": "ENSP00000499136.1",
"transcript_support_level": null,
"aa_start": 806,
"aa_end": null,
"aa_length": 932,
"cds_start": 2416,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652515.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2290G>A",
"hgvs_p": "p.Gly764Arg",
"transcript": "ENST00000890520.1",
"protein_id": "ENSP00000560579.1",
"transcript_support_level": null,
"aa_start": 764,
"aa_end": null,
"aa_length": 890,
"cds_start": 2290,
"cds_end": null,
"cds_length": 2673,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890520.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2287G>A",
"hgvs_p": "p.Gly763Arg",
"transcript": "ENST00000890519.1",
"protein_id": "ENSP00000560578.1",
"transcript_support_level": null,
"aa_start": 763,
"aa_end": null,
"aa_length": 889,
"cds_start": 2287,
"cds_end": null,
"cds_length": 2670,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890519.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.145G>A",
"hgvs_p": "p.Gly49Arg",
"transcript": "ENST00000548418.1",
"protein_id": "ENSP00000447464.1",
"transcript_support_level": 3,
"aa_start": 49,
"aa_end": null,
"aa_length": 91,
"cds_start": 145,
"cds_end": null,
"cds_length": 276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548418.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.2050G>A",
"hgvs_p": "p.Gly684Arg",
"transcript": "XM_047428406.1",
"protein_id": "XP_047284362.1",
"transcript_support_level": null,
"aa_start": 684,
"aa_end": null,
"aa_length": 810,
"cds_start": 2050,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428406.1"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "c.1951G>A",
"hgvs_p": "p.Gly651Arg",
"transcript": "XM_047428407.1",
"protein_id": "XP_047284363.1",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 777,
"cds_start": 1951,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428407.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NOPCHAP1",
"gene_hgnc_id": 28628,
"hgvs_c": "c.*31-28641C>T",
"hgvs_p": null,
"transcript": "ENST00000622317.5",
"protein_id": "ENSP00000477543.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000622317.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NOPCHAP1",
"gene_hgnc_id": 28628,
"hgvs_c": "c.*31-15663C>T",
"hgvs_p": null,
"transcript": "ENST00000637147.1",
"protein_id": "ENSP00000490540.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": null,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000637147.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NOPCHAP1",
"gene_hgnc_id": 28628,
"hgvs_c": "c.*31-17810C>T",
"hgvs_p": null,
"transcript": "ENST00000548583.1",
"protein_id": "ENSP00000490736.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 93,
"cds_start": null,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548583.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "n.2380G>A",
"hgvs_p": null,
"transcript": "ENST00000549335.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000549335.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "n.*1729G>A",
"hgvs_p": null,
"transcript": "ENST00000552270.1",
"protein_id": "ENSP00000447538.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000552270.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "n.2363G>A",
"hgvs_p": null,
"transcript": "NR_027752.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027752.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"hgvs_c": "n.*1729G>A",
"hgvs_p": null,
"transcript": "ENST00000552270.1",
"protein_id": "ENSP00000447538.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000552270.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NOPCHAP1",
"gene_hgnc_id": 28628,
"hgvs_c": "n.*30+35764C>T",
"hgvs_p": null,
"transcript": "ENST00000547750.2",
"protein_id": "ENSP00000490830.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000547750.2"
}
],
"gene_symbol": "ALDH1L2",
"gene_hgnc_id": 26777,
"dbsnp": null,
"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": 0.9938126802444458,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.901,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8292,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.834,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001034173.4",
"gene_symbol": "ALDH1L2",
"hgnc_id": 26777,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2389G>A",
"hgvs_p": "p.Gly797Arg"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000548583.1",
"gene_symbol": "NOPCHAP1",
"hgnc_id": 28628,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*31-17810C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}