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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: 14-67382523-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=67382523&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EIF2S1",
"hgnc_id": 3265,
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_004094.5",
"verdict": "Benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "GPHN",
"hgnc_id": 15465,
"hgvs_c": "c.1312+323737G>A",
"hgvs_p": null,
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -6,
"transcript": "XM_047430879.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_score": -10,
"allele_count_reference_population": 16,
"alphamissense_prediction": null,
"alphamissense_score": 0.0603,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"chr": "14",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.023950040340423584,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4154,
"cdna_start": 885,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_004094.5",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000256383.11",
"protein_coding": true,
"protein_id": "NP_004085.1",
"strand": true,
"transcript": "NM_004094.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4154,
"cdna_start": 885,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000256383.11",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004094.5",
"protein_coding": true,
"protein_id": "ENSP00000256383.4",
"strand": true,
"transcript": "ENST00000256383.11",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2390,
"cdna_start": 1515,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000466499.6",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000425299.1",
"strand": true,
"transcript": "ENST00000466499.6",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 352,
"aa_ref": "S",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1586,
"cdna_start": 976,
"cds_end": null,
"cds_length": 1059,
"cds_start": 866,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000858845.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.866G>A",
"hgvs_p": "p.Ser289Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528904.1",
"strand": true,
"transcript": "ENST00000858845.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 329,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1531,
"cdna_start": 880,
"cds_end": null,
"cds_length": 990,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000950584.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620643.1",
"strand": true,
"transcript": "ENST00000950584.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 325,
"aa_ref": "S",
"aa_start": 262,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1525,
"cdna_start": 915,
"cds_end": null,
"cds_length": 978,
"cds_start": 785,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000858844.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.785G>A",
"hgvs_p": "p.Ser262Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528903.1",
"strand": true,
"transcript": "ENST00000858844.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2729,
"cdna_start": 1706,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000858843.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528902.1",
"strand": true,
"transcript": "ENST00000858843.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1581,
"cdna_start": 968,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000916140.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586199.1",
"strand": true,
"transcript": "ENST00000916140.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 315,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1555,
"cdna_start": 942,
"cds_end": null,
"cds_length": 948,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000916141.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000586200.1",
"strand": true,
"transcript": "ENST00000916141.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 308,
"aa_ref": "S",
"aa_start": 245,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4445,
"cdna_start": 1177,
"cds_end": null,
"cds_length": 927,
"cds_start": 734,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000858842.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.734G>A",
"hgvs_p": "p.Ser245Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528901.1",
"strand": true,
"transcript": "ENST00000858842.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 298,
"aa_ref": "S",
"aa_start": 235,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1414,
"cdna_start": 804,
"cds_end": null,
"cds_length": 897,
"cds_start": 704,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000858846.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.704G>A",
"hgvs_p": "p.Ser235Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000528905.1",
"strand": true,
"transcript": "ENST00000858846.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 291,
"aa_ref": "S",
"aa_start": 228,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1420,
"cdna_start": 809,
"cds_end": null,
"cds_length": 876,
"cds_start": 683,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000950583.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Ser228Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000620642.1",
"strand": true,
"transcript": "ENST00000950583.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 272,
"aa_ref": "S",
"aa_start": 252,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 999,
"cdna_start": 935,
"cds_end": null,
"cds_length": 819,
"cds_start": 755,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000557310.5",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.755G>A",
"hgvs_p": "p.Ser252Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000451975.1",
"strand": true,
"transcript": "ENST00000557310.5",
"transcript_support_level": 2
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 251,
"aa_ref": "S",
"aa_start": 208,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 783,
"cdna_start": 625,
"cds_end": null,
"cds_length": 756,
"cds_start": 623,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000555876.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "c.623G>A",
"hgvs_p": "p.Ser208Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452034.1",
"strand": true,
"transcript": "ENST00000555876.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 485,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1854,
"cdna_start": null,
"cds_end": null,
"cds_length": 1458,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047430879.1",
"gene_hgnc_id": 15465,
"gene_symbol": "GPHN",
"hgvs_c": "c.1312+323737G>A",
"hgvs_p": null,
"intron_rank": 14,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286835.1",
"strand": true,
"transcript": "XM_047430879.1",
"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": 534,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000554332.1",
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"hgvs_c": "n.113G>A",
"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": "ENST00000554332.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199608296",
"effect": "missense_variant",
"frequency_reference_population": 0.0000099135905,
"gene_hgnc_id": 3265,
"gene_symbol": "EIF2S1",
"gnomad_exomes_ac": 14,
"gnomad_exomes_af": 0.00000957751,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131416,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.227,
"pos": 67382523,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.105,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004094.5"
}
]
}