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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: 2-196897132-TGTTTA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196897132&ref=TGTTTA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"gene_symbol": "PGAP1",
"hgnc_id": 25712,
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_024989.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "2",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " autosomal recessive 42,Cerebral visual impairment and intellectual disability,Intellectual disability",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 922,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11090,
"cdna_start": 1016,
"cds_end": null,
"cds_length": 2769,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 27,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_024989.4",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000354764.9",
"protein_coding": true,
"protein_id": "NP_079265.2",
"strand": false,
"transcript": "NM_024989.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 922,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 11090,
"cdna_start": 1016,
"cds_end": null,
"cds_length": 2769,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 27,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000354764.9",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024989.4",
"protein_coding": true,
"protein_id": "ENSP00000346809.3",
"strand": false,
"transcript": "ENST00000354764.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 8942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000423035.5",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.*852_*856delTAAAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415405.1",
"strand": false,
"transcript": "ENST00000423035.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1222,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000485830.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.1065_1069delTAAAC",
"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": "ENST00000485830.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 8942,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 28,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000423035.5",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.*852_*856delTAAAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415405.1",
"strand": false,
"transcript": "ENST00000423035.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 953,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5566,
"cdna_start": 1056,
"cds_end": null,
"cds_length": 2862,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 28,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000961224.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631283.1",
"strand": false,
"transcript": "ENST00000961224.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 876,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3816,
"cdna_start": 1038,
"cds_end": null,
"cds_length": 2631,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 27,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000911521.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581580.1",
"strand": false,
"transcript": "ENST00000911521.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 868,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7693,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 2607,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 25,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000862441.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532500.1",
"strand": false,
"transcript": "ENST00000862441.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 748,
"aa_ref": "TKQ",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11174,
"cdna_start": 1100,
"cds_end": null,
"cds_length": 2247,
"cds_start": 399,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 28,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001321099.2",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.399_403delTAAAC",
"hgvs_p": "p.Lys134fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308028.1",
"strand": false,
"transcript": "NM_001321099.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 592,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2443,
"cdna_start": 1039,
"cds_end": null,
"cds_length": 1779,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 20,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000409475.5",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387028.1",
"strand": false,
"transcript": "ENST00000409475.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 533,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11034,
"cdna_start": null,
"cds_end": null,
"cds_length": 1602,
"cds_start": null,
"consequences": [
"splice_region_variant"
],
"exon_count": 26,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001321100.2",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.-191_-187delTAAAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308029.1",
"strand": false,
"transcript": "NM_001321100.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 181,
"aa_ref": "TKQ",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 677,
"cdna_start": 394,
"cds_end": null,
"cds_length": 548,
"cds_start": 261,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000374738.3",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.261_265delTAAAC",
"hgvs_p": "p.Lys88fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000363870.3",
"strand": false,
"transcript": "ENST00000374738.3",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 748,
"aa_ref": "TKQ",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10945,
"cdna_start": 871,
"cds_end": null,
"cds_length": 2247,
"cds_start": 399,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 27,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_017004992.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.399_403delTAAAC",
"hgvs_p": "p.Lys134fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016860481.1",
"strand": false,
"transcript": "XM_017004992.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 748,
"aa_ref": "TKQ",
"aa_start": 133,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11514,
"cdna_start": 1440,
"cds_end": null,
"cds_length": 2247,
"cds_start": 399,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 28,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_017004993.2",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.399_403delTAAAC",
"hgvs_p": "p.Lys134fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016860482.1",
"strand": false,
"transcript": "XM_017004993.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 452,
"aa_ref": "TKQ",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3279,
"cdna_start": 1016,
"cds_end": null,
"cds_length": 1359,
"cds_start": 921,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 14,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047445910.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.921_925delTAAAC",
"hgvs_p": "p.Lys308fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301866.1",
"strand": false,
"transcript": "XM_047445910.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 533,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11034,
"cdna_start": null,
"cds_end": null,
"cds_length": 1602,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 26,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001321100.2",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "c.-191_-187delTAAAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001308029.1",
"strand": false,
"transcript": "NM_001321100.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1246,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000409188.5",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.795_799delTAAAC",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000386802.1",
"strand": false,
"transcript": "ENST00000409188.5",
"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": 2874,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000470179.5",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.385_389delTAAAC",
"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": "ENST00000470179.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1528,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_001738960.2",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.1012_1016delTAAAC",
"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": "XR_001738960.2",
"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": 2049,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_007082522.1",
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"hgvs_c": "n.1012_1016delTAAAC",
"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": "XR_007082522.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs869025580",
"effect": "frameshift_variant,splice_region_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 25712,
"gene_symbol": "PGAP1",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"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": "Pathogenic",
"phenotype_combined": "Intellectual disability, autosomal recessive 42|Cerebral visual impairment and intellectual disability",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.785,
"pos": 196897132,
"ref": "TGTTTA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_024989.4"
}
]
}