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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: X-50607995-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=50607995&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 50607995,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020717.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3147G>A",
"hgvs_p": "p.Met1049Ile",
"transcript": "NM_020717.5",
"protein_id": "NP_065768.2",
"transcript_support_level": null,
"aa_start": 1049,
"aa_end": null,
"aa_length": 1493,
"cds_start": 3147,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000376020.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020717.5"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3147G>A",
"hgvs_p": "p.Met1049Ile",
"transcript": "ENST00000376020.9",
"protein_id": "ENSP00000365188.2",
"transcript_support_level": 2,
"aa_start": 1049,
"aa_end": null,
"aa_length": 1493,
"cds_start": 3147,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020717.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376020.9"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3147G>A",
"hgvs_p": "p.Met1049Ile",
"transcript": "ENST00000289292.11",
"protein_id": "ENSP00000289292.7",
"transcript_support_level": 1,
"aa_start": 1049,
"aa_end": null,
"aa_length": 1493,
"cds_start": 3147,
"cds_end": null,
"cds_length": 4482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000289292.11"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3012G>A",
"hgvs_p": "p.Met1004Ile",
"transcript": "ENST00000898514.1",
"protein_id": "ENSP00000568573.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3012,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898514.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.2799G>A",
"hgvs_p": "p.Met933Ile",
"transcript": "ENST00000460112.3",
"protein_id": "ENSP00000421450.1",
"transcript_support_level": 5,
"aa_start": 933,
"aa_end": null,
"aa_length": 1377,
"cds_start": 2799,
"cds_end": null,
"cds_length": 4134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000460112.3"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3261G>A",
"hgvs_p": "p.Met1087Ile",
"transcript": "XM_017029682.3",
"protein_id": "XP_016885171.1",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 1531,
"cds_start": 3261,
"cds_end": null,
"cds_length": 4596,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029682.3"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3126G>A",
"hgvs_p": "p.Met1042Ile",
"transcript": "XM_017029683.2",
"protein_id": "XP_016885172.1",
"transcript_support_level": null,
"aa_start": 1042,
"aa_end": null,
"aa_length": 1486,
"cds_start": 3126,
"cds_end": null,
"cds_length": 4461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029683.2"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3012G>A",
"hgvs_p": "p.Met1004Ile",
"transcript": "XM_047442279.1",
"protein_id": "XP_047298235.1",
"transcript_support_level": null,
"aa_start": 1004,
"aa_end": null,
"aa_length": 1448,
"cds_start": 3012,
"cds_end": null,
"cds_length": 4347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442279.1"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.2913G>A",
"hgvs_p": "p.Met971Ile",
"transcript": "XM_017029684.2",
"protein_id": "XP_016885173.1",
"transcript_support_level": null,
"aa_start": 971,
"aa_end": null,
"aa_length": 1415,
"cds_start": 2913,
"cds_end": null,
"cds_length": 4248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029684.2"
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "c.3261G>A",
"hgvs_p": "p.Met1087Ile",
"transcript": "XM_017029685.3",
"protein_id": "XP_016885174.1",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 1398,
"cds_start": 3261,
"cds_end": null,
"cds_length": 4197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029685.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3323G>A",
"hgvs_p": null,
"transcript": "NR_027121.3",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027121.3"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3188G>A",
"hgvs_p": null,
"transcript": "NR_172068.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_172068.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3243G>A",
"hgvs_p": null,
"transcript": "NR_172069.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_172069.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3108G>A",
"hgvs_p": null,
"transcript": "NR_172070.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_172070.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3437G>A",
"hgvs_p": null,
"transcript": "XR_001755716.3",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001755716.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3437G>A",
"hgvs_p": null,
"transcript": "XR_001755717.3",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001755717.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3437G>A",
"hgvs_p": null,
"transcript": "XR_001755718.3",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001755718.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3323G>A",
"hgvs_p": null,
"transcript": "XR_007068196.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007068196.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"hgvs_c": "n.3188G>A",
"hgvs_p": null,
"transcript": "XR_007068197.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007068197.1"
}
],
"gene_symbol": "SHROOM4",
"gene_hgnc_id": 29215,
"dbsnp": "rs61753876",
"frequency_reference_population": 0.0021642,
"hom_count_reference_population": 726,
"allele_count_reference_population": 2619,
"gnomad_exomes_af": 0.00128666,
"gnomad_genomes_af": 0.0107722,
"gnomad_exomes_ac": 1413,
"gnomad_genomes_ac": 1206,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 18,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.00263097882270813,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.056,
"revel_prediction": "Benign",
"alphamissense_score": 0.1913,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.93,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.229,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_020717.5",
"gene_symbol": "SHROOM4",
"hgnc_id": 29215,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3147G>A",
"hgvs_p": "p.Met1049Ile"
}
],
"clinvar_disease": "History of neurodevelopmental disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided|History of neurodevelopmental disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}