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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: 16-53602088-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=53602088&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "RPGRIP1L",
"hgnc_id": 29168,
"hgvs_c": "c.3936C>T",
"hgvs_p": "p.Asp1312Asp",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_015272.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_score": -21,
"allele_count_reference_population": 78401,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.85,
"chr": "16",
"clinvar_classification": "Benign",
"clinvar_disease": " type 5,Joubert syndrome,Joubert syndrome 7,Meckel syndrome,Meckel-Gruber syndrome,Nephronophthisis 8,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:9",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8500000238418579,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1315,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7935,
"cdna_start": 4000,
"cds_end": null,
"cds_length": 3948,
"cds_start": 3936,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "NM_015272.5",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3936C>T",
"hgvs_p": "p.Asp1312Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000647211.2",
"protein_coding": true,
"protein_id": "NP_056087.2",
"strand": false,
"transcript": "NM_015272.5",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1315,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7935,
"cdna_start": 4000,
"cds_end": null,
"cds_length": 3948,
"cds_start": 3936,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000647211.2",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3936C>T",
"hgvs_p": "p.Asp1312Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015272.5",
"protein_coding": true,
"protein_id": "ENSP00000493946.1",
"strand": false,
"transcript": "ENST00000647211.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1281,
"aa_ref": "D",
"aa_start": 1278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4193,
"cdna_start": 3886,
"cds_end": null,
"cds_length": 3846,
"cds_start": 3834,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000563746.5",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3834C>T",
"hgvs_p": "p.Asp1278Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457889.1",
"strand": false,
"transcript": "ENST00000563746.5",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1269,
"aa_ref": "D",
"aa_start": 1266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6678,
"cdna_start": 3844,
"cds_end": null,
"cds_length": 3810,
"cds_start": 3798,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000621565.5",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3798C>T",
"hgvs_p": "p.Asp1266Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000480698.1",
"strand": false,
"transcript": "ENST00000621565.5",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1281,
"aa_ref": "D",
"aa_start": 1278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7833,
"cdna_start": 3898,
"cds_end": null,
"cds_length": 3846,
"cds_start": 3834,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_001330538.2",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3834C>T",
"hgvs_p": "p.Asp1278Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317467.1",
"strand": false,
"transcript": "NM_001330538.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1273,
"aa_ref": "D",
"aa_start": 1270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4488,
"cdna_start": 3857,
"cds_end": null,
"cds_length": 3822,
"cds_start": 3810,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000944945.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3810C>T",
"hgvs_p": "p.Asp1270Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000615004.1",
"strand": false,
"transcript": "ENST00000944945.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1269,
"aa_ref": "D",
"aa_start": 1266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7797,
"cdna_start": 3862,
"cds_end": null,
"cds_length": 3810,
"cds_start": 3798,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_001308334.3",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3798C>T",
"hgvs_p": "p.Asp1266Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001295263.1",
"strand": false,
"transcript": "NM_001308334.3",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1235,
"aa_ref": "D",
"aa_start": 1232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7695,
"cdna_start": 3760,
"cds_end": null,
"cds_length": 3708,
"cds_start": 3696,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "NM_001127897.4",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3696C>T",
"hgvs_p": "p.Asp1232Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001121369.1",
"strand": false,
"transcript": "NM_001127897.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1235,
"aa_ref": "D",
"aa_start": 1232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7725,
"cdna_start": 3790,
"cds_end": null,
"cds_length": 3708,
"cds_start": 3696,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000262135.9",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3696C>T",
"hgvs_p": "p.Asp1232Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000262135.4",
"strand": false,
"transcript": "ENST00000262135.9",
"transcript_support_level": 5
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1207,
"aa_ref": "D",
"aa_start": 1204,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4307,
"cdna_start": 3669,
"cds_end": null,
"cds_length": 3624,
"cds_start": 3612,
"consequences": [
"synonymous_variant"
],
"exon_count": 24,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000935860.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3612C>T",
"hgvs_p": "p.Asp1204Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605919.1",
"strand": false,
"transcript": "ENST00000935860.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1319,
"aa_ref": "D",
"aa_start": 1316,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8195,
"cdna_start": 4260,
"cds_end": null,
"cds_length": 3960,
"cds_start": 3948,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "XM_047433869.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3948C>T",
"hgvs_p": "p.Asp1316Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289825.1",
"strand": false,
"transcript": "XM_047433869.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1315,
"aa_ref": "D",
"aa_start": 1312,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8183,
"cdna_start": 4248,
"cds_end": null,
"cds_length": 3948,
"cds_start": 3936,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "XM_047433870.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3936C>T",
"hgvs_p": "p.Asp1312Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289826.1",
"strand": false,
"transcript": "XM_047433870.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1281,
"aa_ref": "D",
"aa_start": 1278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8081,
"cdna_start": 4146,
"cds_end": null,
"cds_length": 3846,
"cds_start": 3834,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_047433871.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3834C>T",
"hgvs_p": "p.Asp1278Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289827.1",
"strand": false,
"transcript": "XM_047433871.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1273,
"aa_ref": "D",
"aa_start": 1270,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7809,
"cdna_start": 3874,
"cds_end": null,
"cds_length": 3822,
"cds_start": 3810,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "XM_005255868.3",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3810C>T",
"hgvs_p": "p.Asp1270Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005255925.1",
"strand": false,
"transcript": "XM_005255868.3",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "D",
"aa_start": 1236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7707,
"cdna_start": 3772,
"cds_end": null,
"cds_length": 3720,
"cds_start": 3708,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_017023095.3",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3708C>T",
"hgvs_p": "p.Asp1236Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878584.1",
"strand": false,
"transcript": "XM_017023095.3",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 1235,
"aa_ref": "D",
"aa_start": 1232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7943,
"cdna_start": 4008,
"cds_end": null,
"cds_length": 3708,
"cds_start": 3696,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_047433872.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.3696C>T",
"hgvs_p": "p.Asp1232Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047289828.1",
"strand": false,
"transcript": "XM_047433872.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 730,
"aa_ref": "D",
"aa_start": 727,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6876,
"cdna_start": 2941,
"cds_end": null,
"cds_length": 2193,
"cds_start": 2181,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_017023098.2",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.2181C>T",
"hgvs_p": "p.Asp727Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878587.1",
"strand": false,
"transcript": "XM_017023098.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 730,
"aa_ref": "D",
"aa_start": 727,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6236,
"cdna_start": 2301,
"cds_end": null,
"cds_length": 2193,
"cds_start": 2181,
"consequences": [
"synonymous_variant"
],
"exon_count": 14,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_017023099.2",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "c.2181C>T",
"hgvs_p": "p.Asp727Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016878588.1",
"strand": false,
"transcript": "XM_017023099.2",
"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": 7194,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000565343.2",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "n.4360C>T",
"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": "ENST00000565343.2",
"transcript_support_level": 5
},
{
"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": 6903,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000680193.1",
"gene_hgnc_id": 29168,
"gene_symbol": "RPGRIP1L",
"hgvs_c": "n.*696C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506379.1",
"strand": false,
"transcript": "ENST00000680193.1",
"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": 4542,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
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{
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"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Meckel syndrome, type 5|Joubert syndrome 7|Nephronophthisis 8|Joubert syndrome;Meckel-Gruber syndrome|Joubert syndrome|not provided",
"phylop100way_prediction": "Benign",
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}
]
}