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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: 2-196841356-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196841356&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 196841356,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_024989.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2647A>G",
"hgvs_p": "p.Thr883Ala",
"transcript": "NM_024989.4",
"protein_id": "NP_079265.2",
"transcript_support_level": null,
"aa_start": 883,
"aa_end": null,
"aa_length": 922,
"cds_start": 2647,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000354764.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024989.4"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2647A>G",
"hgvs_p": "p.Thr883Ala",
"transcript": "ENST00000354764.9",
"protein_id": "ENSP00000346809.3",
"transcript_support_level": 1,
"aa_start": 883,
"aa_end": null,
"aa_length": 922,
"cds_start": 2647,
"cds_end": null,
"cds_length": 2769,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024989.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000354764.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*2578A>G",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"transcript_support_level": 1,
"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": "ENST00000423035.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*2578A>G",
"hgvs_p": null,
"transcript": "ENST00000423035.5",
"protein_id": "ENSP00000415405.1",
"transcript_support_level": 1,
"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": "ENST00000423035.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2740A>G",
"hgvs_p": "p.Thr914Ala",
"transcript": "ENST00000961224.1",
"protein_id": "ENSP00000631283.1",
"transcript_support_level": null,
"aa_start": 914,
"aa_end": null,
"aa_length": 953,
"cds_start": 2740,
"cds_end": null,
"cds_length": 2862,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961224.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2509A>G",
"hgvs_p": "p.Thr837Ala",
"transcript": "ENST00000911521.1",
"protein_id": "ENSP00000581580.1",
"transcript_support_level": null,
"aa_start": 837,
"aa_end": null,
"aa_length": 876,
"cds_start": 2509,
"cds_end": null,
"cds_length": 2631,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911521.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2485A>G",
"hgvs_p": "p.Thr829Ala",
"transcript": "ENST00000862441.1",
"protein_id": "ENSP00000532500.1",
"transcript_support_level": null,
"aa_start": 829,
"aa_end": null,
"aa_length": 868,
"cds_start": 2485,
"cds_end": null,
"cds_length": 2607,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862441.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2125A>G",
"hgvs_p": "p.Thr709Ala",
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 748,
"cds_start": 2125,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321099.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1480A>G",
"hgvs_p": "p.Thr494Ala",
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 533,
"cds_start": 1480,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321100.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.358A>G",
"hgvs_p": "p.Thr120Ala",
"transcript": "ENST00000422444.1",
"protein_id": "ENSP00000390555.1",
"transcript_support_level": 2,
"aa_start": 120,
"aa_end": null,
"aa_length": 159,
"cds_start": 358,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422444.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2125A>G",
"hgvs_p": "p.Thr709Ala",
"transcript": "XM_017004992.1",
"protein_id": "XP_016860481.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 748,
"cds_start": 2125,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004992.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.2125A>G",
"hgvs_p": "p.Thr709Ala",
"transcript": "XM_017004993.2",
"protein_id": "XP_016860482.1",
"transcript_support_level": null,
"aa_start": 709,
"aa_end": null,
"aa_length": 748,
"cds_start": 2125,
"cds_end": null,
"cds_length": 2247,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004993.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.2857A>G",
"hgvs_p": null,
"transcript": "ENST00000470179.5",
"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": "ENST00000470179.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.105+1365A>G",
"hgvs_p": null,
"transcript": "ENST00000459896.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000459896.5"
}
],
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"dbsnp": "rs139107571",
"frequency_reference_population": 0.0004258437,
"hom_count_reference_population": 3,
"allele_count_reference_population": 687,
"gnomad_exomes_af": 0.000425029,
"gnomad_genomes_af": 0.000433668,
"gnomad_exomes_ac": 621,
"gnomad_genomes_ac": 66,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003011077642440796,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.04,
"revel_prediction": "Benign",
"alphamissense_score": 0.0509,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.24,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_024989.4",
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2647A>G",
"hgvs_p": "p.Thr883Ala"
}
],
"clinvar_disease": " autosomal recessive 42,Hereditary spastic paraplegia,Intellectual disability",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"phenotype_combined": "Intellectual disability, autosomal recessive 42|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}