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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: 2-196875774-CTGTA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196875774&ref=CTGTA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 196875774,
"ref": "CTGTA",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "NM_024989.4",
"consequences": [
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs",
"transcript": "NM_024989.4",
"protein_id": "NP_079265.2",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 922,
"cds_start": 1394,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 1488,
"cdna_end": null,
"cdna_length": 11090,
"mane_select": "ENST00000354764.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024989.4"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs",
"transcript": "ENST00000354764.9",
"protein_id": "ENSP00000346809.3",
"transcript_support_level": 1,
"aa_start": 465,
"aa_end": null,
"aa_length": 922,
"cds_start": 1394,
"cds_end": null,
"cds_length": 2769,
"cdna_start": 1488,
"cdna_end": null,
"cdna_length": 11090,
"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": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*1325_*1328delTACA",
"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": 8942,
"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": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*1325_*1328delTACA",
"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": 8942,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000423035.5"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs",
"transcript": "ENST00000961224.1",
"protein_id": "ENSP00000631283.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 953,
"cds_start": 1394,
"cds_end": null,
"cds_length": 2862,
"cdna_start": 1528,
"cdna_end": null,
"cdna_length": 5566,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000961224.1"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs",
"transcript": "ENST00000911521.1",
"protein_id": "ENSP00000581580.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 876,
"cds_start": 1394,
"cds_end": null,
"cds_length": 2631,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 3816,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911521.1"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1232_1235delTACA",
"hgvs_p": "p.Ile411fs",
"transcript": "ENST00000862441.1",
"protein_id": "ENSP00000532500.1",
"transcript_support_level": null,
"aa_start": 411,
"aa_end": null,
"aa_length": 868,
"cds_start": 1232,
"cds_end": null,
"cds_length": 2607,
"cdna_start": 1349,
"cdna_end": null,
"cdna_length": 7693,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862441.1"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.872_875delTACA",
"hgvs_p": "p.Ile291fs",
"transcript": "NM_001321099.2",
"protein_id": "NP_001308028.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 748,
"cds_start": 872,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1572,
"cdna_end": null,
"cdna_length": 11174,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321099.2"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs",
"transcript": "ENST00000409475.5",
"protein_id": "ENSP00000387028.1",
"transcript_support_level": 2,
"aa_start": 465,
"aa_end": null,
"aa_length": 592,
"cds_start": 1394,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 1511,
"cdna_end": null,
"cdna_length": 2443,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409475.5"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.227_230delTACA",
"hgvs_p": "p.Ile76fs",
"transcript": "NM_001321100.2",
"protein_id": "NP_001308029.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 533,
"cds_start": 227,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 11034,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001321100.2"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.872_875delTACA",
"hgvs_p": "p.Ile291fs",
"transcript": "XM_017004992.1",
"protein_id": "XP_016860481.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 748,
"cds_start": 872,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1343,
"cdna_end": null,
"cdna_length": 10945,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004992.1"
},
{
"aa_ref": "IQ",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.872_875delTACA",
"hgvs_p": "p.Ile291fs",
"transcript": "XM_017004993.2",
"protein_id": "XP_016860482.1",
"transcript_support_level": null,
"aa_start": 291,
"aa_end": null,
"aa_length": 748,
"cds_start": 872,
"cds_end": null,
"cds_length": 2247,
"cdna_start": 1912,
"cdna_end": null,
"cdna_length": 11514,
"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": 10,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.858_861delTACA",
"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": 2874,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.315_318delTACA",
"hgvs_p": null,
"transcript": "ENST00000482051.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 540,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000482051.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.1485_1488delTACA",
"hgvs_p": null,
"transcript": "XR_007082522.1",
"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": 2049,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007082522.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "c.*1850_*1853delTACA",
"hgvs_p": null,
"transcript": "XM_047445910.1",
"protein_id": "XP_047301866.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 452,
"cds_start": null,
"cds_end": null,
"cds_length": 1359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445910.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"hgvs_c": "n.*21_*24delTACA",
"hgvs_p": null,
"transcript": "XR_001738960.2",
"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": 1528,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001738960.2"
}
],
"gene_symbol": "PGAP1",
"gene_hgnc_id": 25712,
"dbsnp": "rs781325598",
"frequency_reference_population": 0.0000038905105,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000215834,
"gnomad_genomes_af": 0.0000197037,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 5.457,
"phylop100way_prediction": "Uncertain_significance",
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_024989.4",
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1394_1397delTACA",
"hgvs_p": "p.Ile465fs"
}
],
"clinvar_disease": " autosomal recessive 42,Intellectual disability,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Intellectual disability, autosomal recessive 42|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}