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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: 5-177332142-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=177332142&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "LMAN2",
"hgnc_id": 16986,
"hgvs_c": "c.1015G>A",
"hgvs_p": "p.Val339Met",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_006816.3",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 31,
"alphamissense_prediction": "Uncertain_significance",
"alphamissense_score": 0.5411,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.02,
"chr": "5",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5518808364868164,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 356,
"aa_ref": "V",
"aa_start": 339,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1611,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1071,
"cds_start": 1015,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_006816.3",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.1015G>A",
"hgvs_p": "p.Val339Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000303127.12",
"protein_coding": true,
"protein_id": "NP_006807.1",
"strand": false,
"transcript": "NM_006816.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 356,
"aa_ref": "V",
"aa_start": 339,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1611,
"cdna_start": 1036,
"cds_end": null,
"cds_length": 1071,
"cds_start": 1015,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000303127.12",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.1015G>A",
"hgvs_p": "p.Val339Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006816.3",
"protein_coding": true,
"protein_id": "ENSP00000303366.7",
"strand": false,
"transcript": "ENST00000303127.12",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 398,
"aa_ref": "V",
"aa_start": 381,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1346,
"cdna_start": 1159,
"cds_end": null,
"cds_length": 1197,
"cds_start": 1141,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000883396.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.1141G>A",
"hgvs_p": "p.Val381Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553455.1",
"strand": false,
"transcript": "ENST00000883396.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 366,
"aa_ref": "V",
"aa_start": 349,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1639,
"cdna_start": 1059,
"cds_end": null,
"cds_length": 1101,
"cds_start": 1045,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000883394.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.1045G>A",
"hgvs_p": "p.Val349Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553453.1",
"strand": false,
"transcript": "ENST00000883394.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 363,
"aa_ref": "V",
"aa_start": 346,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1629,
"cdna_start": 1050,
"cds_end": null,
"cds_length": 1092,
"cds_start": 1036,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000883395.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.1036G>A",
"hgvs_p": "p.Val346Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553454.1",
"strand": false,
"transcript": "ENST00000883395.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 347,
"aa_ref": "V",
"aa_start": 330,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1584,
"cdna_start": 1009,
"cds_end": null,
"cds_length": 1044,
"cds_start": 988,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000883393.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.988G>A",
"hgvs_p": "p.Val330Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000553452.1",
"strand": false,
"transcript": "ENST00000883393.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 325,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1149,
"cdna_start": null,
"cds_end": null,
"cds_length": 978,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000515209.5",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.*60G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423998.1",
"strand": false,
"transcript": "ENST00000515209.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 317,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3618,
"cdna_start": null,
"cds_end": null,
"cds_length": 954,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000694905.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.*2098G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000511580.1",
"strand": false,
"transcript": "ENST00000694905.1",
"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": 4339,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000502721.6",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "n.3776G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000502721.6",
"transcript_support_level": 3
},
{
"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": 562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000504071.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "n.374G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000504071.1",
"transcript_support_level": 2
},
{
"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": 3184,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000694904.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "n.2617G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000694904.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3087,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000694903.1",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "n.1103+2142G>A",
"hgvs_p": null,
"intron_rank": 7,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000694903.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 202,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 616,
"cdna_start": null,
"cds_end": null,
"cds_length": 611,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000514458.5",
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"hgvs_c": "c.*60G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424132.1",
"strand": true,
"transcript": "ENST00000514458.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs368637534",
"effect": "missense_variant",
"frequency_reference_population": 0.000019211915,
"gene_hgnc_id": 16986,
"gene_symbol": "LMAN2",
"gnomad_exomes_ac": 27,
"gnomad_exomes_af": 0.0000184758,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 4,
"gnomad_genomes_af": 0.0000262791,
"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": null,
"phenotype_combined": null,
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"pos": 177332142,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.308,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_006816.3"
}
]
}