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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: 1-155904475-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=155904475&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "RIT1",
"hgnc_id": 10023,
"hgvs_c": "c.316T>C",
"hgvs_p": "p.Tyr106His",
"inheritance_mode": "AD",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_001256821.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_score": 20,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.9971,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.39,
"chr": "1",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Noonan syndrome,Noonan syndrome 8,Noonan syndrome and Noonan-related syndrome,RIT1-related disorder,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9605548977851868,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 219,
"aa_ref": "Y",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3390,
"cdna_start": 415,
"cds_end": null,
"cds_length": 660,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_006912.6",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.265T>C",
"hgvs_p": "p.Tyr89His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000368323.8",
"protein_coding": true,
"protein_id": "NP_008843.1",
"strand": false,
"transcript": "NM_006912.6",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 219,
"aa_ref": "Y",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3390,
"cdna_start": 415,
"cds_end": null,
"cds_length": 660,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000368323.8",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.265T>C",
"hgvs_p": "p.Tyr89His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006912.6",
"protein_coding": true,
"protein_id": "ENSP00000357306.3",
"strand": false,
"transcript": "ENST00000368323.8",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 150,
"aa_ref": "Y",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 574,
"cdna_start": 385,
"cds_end": null,
"cds_length": 454,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000609492.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.265T>C",
"hgvs_p": "p.Tyr89His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000476612.1",
"strand": false,
"transcript": "ENST00000609492.1",
"transcript_support_level": 1
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "Y",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3324,
"cdna_start": 349,
"cds_end": null,
"cds_length": 711,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001256821.2",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.316T>C",
"hgvs_p": "p.Tyr106His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243750.1",
"strand": false,
"transcript": "NM_001256821.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 236,
"aa_ref": "Y",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 855,
"cdna_start": 346,
"cds_end": null,
"cds_length": 711,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000368322.7",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.316T>C",
"hgvs_p": "p.Tyr106His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000357305.3",
"strand": false,
"transcript": "ENST00000368322.7",
"transcript_support_level": 3
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 220,
"aa_ref": "Y",
"aa_start": 90,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2419,
"cdna_start": 473,
"cds_end": null,
"cds_length": 663,
"cds_start": 268,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000651853.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.268T>C",
"hgvs_p": "p.Tyr90His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498685.1",
"strand": false,
"transcript": "ENST00000651853.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 219,
"aa_ref": "Y",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2204,
"cdna_start": 469,
"cds_end": null,
"cds_length": 660,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000912983.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.265T>C",
"hgvs_p": "p.Tyr89His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583042.1",
"strand": false,
"transcript": "ENST00000912983.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 218,
"aa_ref": "Y",
"aa_start": 88,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1637,
"cdna_start": 391,
"cds_end": null,
"cds_length": 657,
"cds_start": 262,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000859070.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.262T>C",
"hgvs_p": "p.Tyr88His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000529129.1",
"strand": false,
"transcript": "ENST00000859070.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 193,
"aa_ref": "Y",
"aa_start": 63,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1001,
"cdna_start": 372,
"cds_end": null,
"cds_length": 582,
"cds_start": 187,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000912984.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.187T>C",
"hgvs_p": "p.Tyr63His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583043.1",
"strand": false,
"transcript": "ENST00000912984.1",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 183,
"aa_ref": "Y",
"aa_start": 53,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3241,
"cdna_start": 266,
"cds_end": null,
"cds_length": 552,
"cds_start": 157,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001256820.2",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.157T>C",
"hgvs_p": "p.Tyr53His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001243749.1",
"strand": false,
"transcript": "NM_001256820.2",
"transcript_support_level": null
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 183,
"aa_ref": "Y",
"aa_start": 53,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2139,
"cdna_start": 268,
"cds_end": null,
"cds_length": 552,
"cds_start": 157,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000539040.6",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.157T>C",
"hgvs_p": "p.Tyr53His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000441950.1",
"strand": false,
"transcript": "ENST00000539040.6",
"transcript_support_level": 2
},
{
"aa_alt": "H",
"aa_end": null,
"aa_length": 121,
"aa_ref": "Y",
"aa_start": 89,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 519,
"cdna_start": 418,
"cds_end": null,
"cds_length": 366,
"cds_start": 265,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000651833.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "c.265T>C",
"hgvs_p": "p.Tyr89His",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498732.1",
"strand": false,
"transcript": "ENST00000651833.1",
"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": 2485,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000461050.6",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "n.273T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000476319.1",
"strand": false,
"transcript": "ENST00000461050.6",
"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": 2256,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000704061.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "n.242T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000515664.1",
"strand": false,
"transcript": "ENST00000704061.1",
"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": 538,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650659.1",
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"hgvs_c": "n.*137T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000650659.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs869025197",
"effect": "missense_variant",
"frequency_reference_population": 6.8411526e-7,
"gene_hgnc_id": 10023,
"gene_symbol": "RIT1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84115e-7,
"gnomad_exomes_homalt": 0,
"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": "Noonan syndrome|Noonan syndrome 8|not provided|Noonan syndrome and Noonan-related syndrome|RIT1-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.553,
"pos": 155904475,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.949,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001256821.2"
}
]
}