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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: 3-132689076-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=132689076&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 132689076,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_153240.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.2881C>G",
"hgvs_p": "p.Gln961Glu",
"transcript": "NM_153240.5",
"protein_id": "NP_694972.3",
"transcript_support_level": null,
"aa_start": 961,
"aa_end": null,
"aa_length": 1330,
"cds_start": 2881,
"cds_end": null,
"cds_length": 3993,
"cdna_start": 2935,
"cdna_end": null,
"cdna_length": 5348,
"mane_select": "ENST00000337331.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153240.5"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.2881C>G",
"hgvs_p": "p.Gln961Glu",
"transcript": "ENST00000337331.10",
"protein_id": "ENSP00000338766.5",
"transcript_support_level": 1,
"aa_start": 961,
"aa_end": null,
"aa_length": 1330,
"cds_start": 2881,
"cds_end": null,
"cds_length": 3993,
"cdna_start": 2935,
"cdna_end": null,
"cdna_length": 5348,
"mane_select": "NM_153240.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000337331.10"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.2680C>G",
"hgvs_p": "p.Gln894Glu",
"transcript": "ENST00000971413.1",
"protein_id": "ENSP00000641472.1",
"transcript_support_level": null,
"aa_start": 894,
"aa_end": null,
"aa_length": 1263,
"cds_start": 2680,
"cds_end": null,
"cds_length": 3792,
"cdna_start": 2754,
"cdna_end": null,
"cdna_length": 4517,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971413.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "c.2458C>G",
"hgvs_p": "p.Gln820Glu",
"transcript": "ENST00000971412.1",
"protein_id": "ENSP00000641471.1",
"transcript_support_level": null,
"aa_start": 820,
"aa_end": null,
"aa_length": 1189,
"cds_start": 2458,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 2514,
"cdna_end": null,
"cdna_length": 4926,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971412.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*789C>G",
"hgvs_p": null,
"transcript": "ENST00000465756.5",
"protein_id": "ENSP00000419907.1",
"transcript_support_level": 5,
"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": 3852,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000465756.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.*872C>G",
"hgvs_p": null,
"transcript": "ENST00000471702.2",
"protein_id": "ENSP00000419763.1",
"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": 7784,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471702.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.615C>G",
"hgvs_p": null,
"transcript": "ENST00000474871.5",
"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": 4493,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000474871.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.3606C>G",
"hgvs_p": null,
"transcript": "ENST00000490993.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 5197,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000490993.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*789C>G",
"hgvs_p": null,
"transcript": "ENST00000684294.1",
"protein_id": "ENSP00000508078.1",
"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": 3872,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000684294.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.2887C>G",
"hgvs_p": null,
"transcript": "NR_037804.1",
"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": 7788,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037804.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*789C>G",
"hgvs_p": null,
"transcript": "ENST00000465756.5",
"protein_id": "ENSP00000419907.1",
"transcript_support_level": 5,
"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": 3852,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000465756.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3-ACAD11",
"gene_hgnc_id": 48351,
"hgvs_c": "n.*872C>G",
"hgvs_p": null,
"transcript": "ENST00000471702.2",
"protein_id": "ENSP00000419763.1",
"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": 7784,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471702.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"hgvs_c": "n.*789C>G",
"hgvs_p": null,
"transcript": "ENST00000684294.1",
"protein_id": "ENSP00000508078.1",
"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": 3872,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000684294.1"
}
],
"gene_symbol": "NPHP3",
"gene_hgnc_id": 7907,
"dbsnp": "rs144989330",
"frequency_reference_population": 0.0005359455,
"hom_count_reference_population": 1,
"allele_count_reference_population": 865,
"gnomad_exomes_af": 0.00055685,
"gnomad_genomes_af": 0.000335138,
"gnomad_exomes_ac": 814,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5835422873497009,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.5879999995231628,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.558,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1395,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.352,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.05,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.929377639841109,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_153240.5",
"gene_symbol": "NPHP3",
"hgnc_id": 7907,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2881C>G",
"hgvs_p": "p.Gln961Glu"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000471702.2",
"gene_symbol": "NPHP3-ACAD11",
"hgnc_id": 48351,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*872C>G",
"hgvs_p": null
}
],
"clinvar_disease": "NPHP3-related Meckel-like syndrome,Nephronophthisis,Nephronophthisis 3,Renal-hepatic-pancreatic dysplasia 1,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:7",
"phenotype_combined": "Nephronophthisis|Renal-hepatic-pancreatic dysplasia 1|NPHP3-related Meckel-like syndrome|Nephronophthisis 3;NPHP3-related Meckel-like syndrome;Renal-hepatic-pancreatic dysplasia 1|Nephronophthisis 3|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}