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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: 4-25145092-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=25145092&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP5"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SEPSECS",
"hgnc_id": 30605,
"hgvs_c": "c.1101G>A",
"hgvs_p": "p.Leu367Leu",
"inheritance_mode": "AR",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_001410714.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM2,PP5",
"acmg_score": 7,
"allele_count_reference_population": 105,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"chr": "4",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Pontocerebellar hypoplasia type 2D,Pontoneocerebellar hypoplasia,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:4 US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4000000059604645,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 501,
"aa_ref": "L",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5503,
"cdna_start": 926,
"cds_end": null,
"cds_length": 1506,
"cds_start": 846,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_016955.4",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.846G>A",
"hgvs_p": "p.Leu282Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000382103.7",
"protein_coding": true,
"protein_id": "NP_058651.3",
"strand": false,
"transcript": "NM_016955.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 501,
"aa_ref": "L",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5503,
"cdna_start": 926,
"cds_end": null,
"cds_length": 1506,
"cds_start": 846,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000382103.7",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.846G>A",
"hgvs_p": "p.Leu282Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_016955.4",
"protein_coding": true,
"protein_id": "ENSP00000371535.2",
"strand": false,
"transcript": "ENST00000382103.7",
"transcript_support_level": 1
},
{
"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": 3344,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000358971.7",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.*644G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000351857.3",
"strand": false,
"transcript": "ENST00000358971.7",
"transcript_support_level": 1
},
{
"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": 1494,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000514585.5",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.*547G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421880.1",
"strand": false,
"transcript": "ENST00000514585.5",
"transcript_support_level": 1
},
{
"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": 3344,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000358971.7",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.*644G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000351857.3",
"strand": false,
"transcript": "ENST00000358971.7",
"transcript_support_level": 1
},
{
"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": 1494,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000514585.5",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.*547G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000421880.1",
"strand": false,
"transcript": "ENST00000514585.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 586,
"aa_ref": "L",
"aa_start": 367,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5758,
"cdna_start": 1181,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1101,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001410714.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.1101G>A",
"hgvs_p": "p.Leu367Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001397643.1",
"strand": false,
"transcript": "NM_001410714.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 586,
"aa_ref": "L",
"aa_start": 367,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5802,
"cdna_start": 1278,
"cds_end": null,
"cds_length": 1761,
"cds_start": 1101,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000681948.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.1101G>A",
"hgvs_p": "p.Leu367Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000505991.1",
"strand": false,
"transcript": "ENST00000681948.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 540,
"aa_ref": "L",
"aa_start": 321,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5617,
"cdna_start": 1042,
"cds_end": null,
"cds_length": 1623,
"cds_start": 963,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000952587.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.963G>A",
"hgvs_p": "p.Leu321Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622646.1",
"strand": false,
"transcript": "ENST00000952587.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 457,
"aa_ref": "L",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3273,
"cdna_start": 723,
"cds_end": null,
"cds_length": 1374,
"cds_start": 714,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000853998.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.714G>A",
"hgvs_p": "p.Leu238Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524057.1",
"strand": false,
"transcript": "ENST00000853998.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 500,
"aa_ref": "L",
"aa_start": 281,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5640,
"cdna_start": 1063,
"cds_end": null,
"cds_length": 1503,
"cds_start": 843,
"consequences": [
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_011513846.3",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.843G>A",
"hgvs_p": "p.Leu281Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512148.1",
"strand": false,
"transcript": "XM_011513846.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 490,
"aa_ref": "L",
"aa_start": 271,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5944,
"cdna_start": 1367,
"cds_end": null,
"cds_length": 1473,
"cds_start": 813,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011513847.3",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Leu271Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512149.1",
"strand": false,
"transcript": "XM_011513847.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 441,
"aa_ref": "L",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5327,
"cdna_start": 750,
"cds_end": null,
"cds_length": 1326,
"cds_start": 666,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011513848.2",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Leu222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011512150.1",
"strand": false,
"transcript": "XM_011513848.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 441,
"aa_ref": "L",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5347,
"cdna_start": 770,
"cds_end": null,
"cds_length": 1326,
"cds_start": 666,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047415762.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.666G>A",
"hgvs_p": "p.Leu222Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271718.1",
"strand": false,
"transcript": "XM_047415762.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 427,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3369,
"cdna_start": null,
"cds_end": null,
"cds_length": 1284,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000853997.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "c.804+6868G>A",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000524056.1",
"strand": false,
"transcript": "ENST00000853997.1",
"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": 5441,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000680581.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.846G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000506483.1",
"strand": false,
"transcript": "ENST00000680581.1",
"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": 6574,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000680824.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.2062G>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": "ENST00000680824.1",
"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": 5646,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000681071.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.1138G>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": "ENST00000681071.1",
"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": 6401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000681341.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.1987G>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": "ENST00000681341.1",
"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": 544,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000503150.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.216-227G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000423850.1",
"strand": false,
"transcript": "ENST00000503150.1",
"transcript_support_level": 4
},
{
"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": 420,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000505513.1",
"gene_hgnc_id": 30605,
"gene_symbol": "SEPSECS",
"hgvs_c": "n.235-227G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
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"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000505513.1",
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}
],
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"effect": "synonymous_variant",
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"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Pontocerebellar hypoplasia type 2D|not provided|Pontoneocerebellar hypoplasia",
"phylop100way_prediction": "Uncertain_significance",
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"ref": "C",
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"splice_prediction_selected": "Uncertain_significance",
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"splice_source_selected": "max_spliceai",
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}
]
}