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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: 4-112431743-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=112431743&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 112431743,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000650871.1",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile",
"transcript": "NM_025144.4",
"protein_id": "NP_079420.3",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 1244,
"cds_start": 2196,
"cds_end": null,
"cds_length": 3735,
"cdna_start": 2449,
"cdna_end": null,
"cdna_length": 5399,
"mane_select": "ENST00000650871.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile",
"transcript": "ENST00000650871.1",
"protein_id": "ENSP00000498374.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 1244,
"cds_start": 2196,
"cds_end": null,
"cds_length": 3735,
"cdna_start": 2449,
"cdna_end": null,
"cdna_length": 5399,
"mane_select": "NM_025144.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile",
"transcript": "ENST00000177648.13",
"protein_id": "ENSP00000177648.9",
"transcript_support_level": 1,
"aa_start": 732,
"aa_end": null,
"aa_length": 1244,
"cds_start": 2196,
"cds_end": null,
"cds_length": 3735,
"cdna_start": 2396,
"cdna_end": null,
"cdna_length": 4537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile",
"transcript": "NM_001102406.2",
"protein_id": "NP_001095876.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 1244,
"cds_start": 2196,
"cds_end": null,
"cds_length": 3735,
"cdna_start": 2397,
"cdna_end": null,
"cdna_length": 5347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile",
"transcript": "ENST00000458497.6",
"protein_id": "ENSP00000398048.1",
"transcript_support_level": 5,
"aa_start": 732,
"aa_end": null,
"aa_length": 1244,
"cds_start": 2196,
"cds_end": null,
"cds_length": 3735,
"cdna_start": 2578,
"cdna_end": null,
"cdna_length": 4566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.1962G>A",
"hgvs_p": "p.Met654Ile",
"transcript": "NM_001253884.2",
"protein_id": "NP_001240813.1",
"transcript_support_level": null,
"aa_start": 654,
"aa_end": null,
"aa_length": 1166,
"cds_start": 1962,
"cds_end": null,
"cds_length": 3501,
"cdna_start": 2242,
"cdna_end": null,
"cdna_length": 5192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "c.1962G>A",
"hgvs_p": "p.Met654Ile",
"transcript": "ENST00000504176.6",
"protein_id": "ENSP00000426044.2",
"transcript_support_level": 2,
"aa_start": 654,
"aa_end": null,
"aa_length": 1166,
"cds_start": 1962,
"cds_end": null,
"cds_length": 3501,
"cdna_start": 2268,
"cdna_end": null,
"cdna_length": 5203,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "n.2684G>A",
"hgvs_p": null,
"transcript": "ENST00000504745.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 5633,
"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": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "n.*1639G>A",
"hgvs_p": null,
"transcript": "ENST00000509722.5",
"protein_id": "ENSP00000424492.1",
"transcript_support_level": 2,
"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": 3931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "n.*1639G>A",
"hgvs_p": null,
"transcript": "ENST00000509722.5",
"protein_id": "ENSP00000424492.1",
"transcript_support_level": 2,
"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": 3931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"hgvs_c": "n.900+2490G>A",
"hgvs_p": null,
"transcript": "ENST00000505127.5",
"protein_id": "ENSP00000425559.1",
"transcript_support_level": 2,
"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": 2295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALPK1",
"gene_hgnc_id": 20917,
"dbsnp": "rs2074379",
"frequency_reference_population": 0.62733376,
"hom_count_reference_population": 318847,
"allele_count_reference_population": 1012454,
"gnomad_exomes_af": 0.625182,
"gnomad_genomes_af": 0.648021,
"gnomad_exomes_ac": 913934,
"gnomad_genomes_ac": 98520,
"gnomad_exomes_homalt": 286797,
"gnomad_genomes_homalt": 32050,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000033397666356904665,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.076,
"revel_prediction": "Benign",
"alphamissense_score": 0.1315,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.76,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.207,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000650871.1",
"gene_symbol": "ALPK1",
"hgnc_id": 20917,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Met732Ile"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}