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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: 19-41354765-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41354765&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41354765,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_030578.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "S",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "NM_030578.4",
"protein_id": "NP_085055.2",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000243578.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030578.4"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": true,
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "ENST00000243578.8",
"protein_id": "ENSP00000243578.2",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_030578.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000243578.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.-30+3563C>T",
"hgvs_p": null,
"transcript": "ENST00000539627.5",
"protein_id": "ENSP00000441900.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 132,
"cds_start": null,
"cds_end": null,
"cds_length": 399,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539627.5"
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "ENST00000675972.1",
"protein_id": "ENSP00000501911.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675972.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "ENST00000890351.1",
"protein_id": "ENSP00000560410.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890351.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "ENST00000932334.1",
"protein_id": "ENSP00000602393.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932334.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.337G>A",
"hgvs_p": "p.Gly113Ser",
"transcript": "ENST00000890348.1",
"protein_id": "ENSP00000560407.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 133,
"cds_start": 337,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890348.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.337G>A",
"hgvs_p": "p.Gly113Ser",
"transcript": "ENST00000890350.1",
"protein_id": "ENSP00000560409.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 133,
"cds_start": 337,
"cds_end": null,
"cds_length": 402,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890350.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.223G>A",
"hgvs_p": "p.Gly75Ser",
"transcript": "ENST00000890349.1",
"protein_id": "ENSP00000560408.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 95,
"cds_start": 223,
"cds_end": null,
"cds_length": 288,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890349.1"
},
{
"aa_ref": "G",
"aa_alt": "S",
"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": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser",
"transcript": "XM_011527349.3",
"protein_id": "XP_011525651.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 175,
"cds_start": 463,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527349.3"
},
{
"aa_ref": "G",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "c.304G>A",
"hgvs_p": "p.Gly102Ser",
"transcript": "XM_011527350.3",
"protein_id": "XP_011525652.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 122,
"cds_start": 304,
"cds_end": null,
"cds_length": 369,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527350.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.142+450C>T",
"hgvs_p": null,
"transcript": "ENST00000604123.5",
"protein_id": "ENSP00000474871.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": null,
"cds_end": null,
"cds_length": 573,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000604123.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.-30+3563C>T",
"hgvs_p": null,
"transcript": "ENST00000889861.1",
"protein_id": "ENSP00000559920.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889861.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.-30+450C>T",
"hgvs_p": null,
"transcript": "ENST00000889862.1",
"protein_id": "ENSP00000559921.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889862.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM91",
"gene_hgnc_id": 32393,
"hgvs_c": "c.-30+1622C>T",
"hgvs_p": null,
"transcript": "ENST00000966284.1",
"protein_id": "ENSP00000636343.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966284.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.*309G>A",
"hgvs_p": null,
"transcript": "ENST00000594416.1",
"protein_id": "ENSP00000469666.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000594416.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"hgvs_c": "n.*309G>A",
"hgvs_p": null,
"transcript": "ENST00000594416.1",
"protein_id": "ENSP00000469666.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000594416.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255730",
"gene_hgnc_id": null,
"hgvs_c": "n.350+3563C>T",
"hgvs_p": null,
"transcript": "ENST00000604424.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000604424.1"
}
],
"gene_symbol": "B9D2",
"gene_hgnc_id": 28636,
"dbsnp": "rs750436680",
"frequency_reference_population": 6.8412834e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84128e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9910171031951904,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.825,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9198,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.378,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PM1",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_030578.4",
"gene_symbol": "B9D2",
"hgnc_id": 28636,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Gly155Ser"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000539627.5",
"gene_symbol": "TMEM91",
"hgnc_id": 32393,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-30+3563C>T",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000604424.1",
"gene_symbol": "ENSG00000255730",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.350+3563C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Joubert syndrome,Joubert syndrome 34,Joubert syndrome and related disorders",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Joubert syndrome|Joubert syndrome 34|Joubert syndrome and related disorders",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}