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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: 2-165323422-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165323422&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 19,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SCN2A",
"hgnc_id": 10588,
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -19,
"transcript": "NM_021007.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -19,
"allele_count_reference_population": 49,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"chr": "2",
"clinvar_classification": "Likely benign",
"clinvar_disease": " 11, 3, benign familial infantile,Developmental and epileptic encephalopathy,Seizures,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.3400000035762787,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8776,
"cdna_start": 2216,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001040142.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000375437.7",
"protein_coding": true,
"protein_id": "NP_001035232.1",
"strand": true,
"transcript": "NM_001040142.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8776,
"cdna_start": 2216,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001371246.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "ENST00000631182.3",
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001358175.1",
"strand": true,
"transcript": "NM_001371246.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8776,
"cdna_start": 2216,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000375437.7",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001040142.2",
"protein_coding": true,
"protein_id": "ENSP00000364586.2",
"strand": true,
"transcript": "ENST00000375437.7",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8776,
"cdna_start": 2216,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000631182.3",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": "NM_001371246.1",
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000486885.1",
"strand": true,
"transcript": "ENST00000631182.3",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8660,
"cdna_start": 2094,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000283256.10",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000283256.6",
"strand": true,
"transcript": "ENST00000283256.10",
"transcript_support_level": 1
},
{
"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": 11676,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000480032.4",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.2081C>T",
"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": "ENST00000480032.4",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8895,
"cdna_start": 2335,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001040143.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001035233.1",
"strand": true,
"transcript": "NM_001040143.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8604,
"cdna_start": 2044,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_001371247.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001358176.1",
"strand": true,
"transcript": "NM_001371247.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8630,
"cdna_start": 2070,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_021007.3",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_066287.2",
"strand": true,
"transcript": "NM_021007.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8881,
"cdna_start": 2315,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000636071.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490107.1",
"strand": true,
"transcript": "ENST00000636071.2",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 2005,
"aa_ref": "S",
"aa_start": 646,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8610,
"cdna_start": 2044,
"cds_end": null,
"cds_length": 6018,
"cds_start": 1938,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000637266.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1938C>T",
"hgvs_p": "p.Ser646Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490866.1",
"strand": true,
"transcript": "ENST00000637266.2",
"transcript_support_level": 5
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 1873,
"aa_ref": "S",
"aa_start": 514,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8856,
"cdna_start": 2290,
"cds_end": null,
"cds_length": 5622,
"cds_start": 1542,
"consequences": [
"synonymous_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000636985.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "c.1542C>T",
"hgvs_p": "p.Ser514Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490849.1",
"strand": true,
"transcript": "ENST00000636985.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3119,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000635945.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.2301C>T",
"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": "ENST00000635945.1",
"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": 8519,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000636135.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.*257C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000489821.1",
"strand": true,
"transcript": "ENST00000636135.1",
"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": 9007,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000636384.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.1938C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490765.1",
"strand": true,
"transcript": "ENST00000636384.2",
"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": 9456,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000636662.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.*2461C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000489873.1",
"strand": true,
"transcript": "ENST00000636662.2",
"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": 8573,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000636769.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.1938C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490800.1",
"strand": true,
"transcript": "ENST00000636769.1",
"transcript_support_level": 5
},
{
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"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4408,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000637367.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.*1871C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490592.1",
"strand": true,
"transcript": "ENST00000637367.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2832,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000638151.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.2022C>T",
"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": "ENST00000638151.1",
"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": 8519,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 28,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000636135.1",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.*257C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000489821.1",
"strand": true,
"transcript": "ENST00000636135.1",
"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": 9456,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 27,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000636662.2",
"gene_hgnc_id": 10588,
"gene_symbol": "SCN2A",
"hgvs_c": "n.*2461C>T",
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{
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],
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}
]
}