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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: 2-39022773-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=39022773&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM1_Strong",
"PP3",
"PP2",
"PS2",
"PM2",
"PS3",
"PS4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SOS1",
"hgnc_id": 11187,
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"inheritance_mode": "AD",
"pathogenic_score": 20,
"score": 20,
"transcript": "NM_005633.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1_Strong,PP3,PP2,PS2,PM2,PS3,PS4",
"acmg_score": 20,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.8272,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.26,
"chr": "2",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " 1, gingival,Fibromatosis,Noonan syndrome,Noonan syndrome 1,Noonan syndrome 3,Noonan syndrome 4,RASopathy,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:14",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8900256752967834,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1333,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8906,
"cdna_start": 2284,
"cds_end": null,
"cds_length": 4002,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_005633.4",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000402219.8",
"protein_coding": true,
"protein_id": "NP_005624.2",
"strand": false,
"transcript": "NM_005633.4",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1333,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 8906,
"cdna_start": 2284,
"cds_end": null,
"cds_length": 4002,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000402219.8",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005633.4",
"protein_coding": true,
"protein_id": "ENSP00000384675.2",
"strand": false,
"transcript": "ENST00000402219.8",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1326,
"aa_ref": "R",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8395,
"cdna_start": 1773,
"cds_end": null,
"cds_length": 3981,
"cds_start": 1634,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001382394.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1634G>A",
"hgvs_p": "p.Arg545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001369323.1",
"strand": false,
"transcript": "NM_001382394.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1318,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8861,
"cdna_start": 2284,
"cds_end": null,
"cds_length": 3957,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001382395.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001369324.1",
"strand": false,
"transcript": "NM_001382395.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1318,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4123,
"cdna_start": 1683,
"cds_end": null,
"cds_length": 3957,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000395038.6",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000378479.2",
"strand": false,
"transcript": "ENST00000395038.6",
"transcript_support_level": 5
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1293,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5600,
"cdna_start": 2243,
"cds_end": null,
"cds_length": 3882,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000913801.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583860.1",
"strand": false,
"transcript": "ENST00000913801.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1278,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8691,
"cdna_start": 2244,
"cds_end": null,
"cds_length": 3837,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000913800.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583859.1",
"strand": false,
"transcript": "ENST00000913800.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1147,
"aa_ref": "R",
"aa_start": 515,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4056,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 3444,
"cds_start": 1544,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000692089.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1544G>A",
"hgvs_p": "p.Arg515Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508626.1",
"strand": false,
"transcript": "ENST00000692089.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1086,
"aa_ref": "R",
"aa_start": 515,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5976,
"cdna_start": 1561,
"cds_end": null,
"cds_length": 3261,
"cds_start": 1544,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000691229.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1544G>A",
"hgvs_p": "p.Arg515Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000510437.1",
"strand": false,
"transcript": "ENST00000691229.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 922,
"aa_ref": "R",
"aa_start": 141,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7030,
"cdna_start": 489,
"cds_end": null,
"cds_length": 2769,
"cds_start": 422,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000685279.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.422G>A",
"hgvs_p": "p.Arg141Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509424.1",
"strand": false,
"transcript": "ENST00000685279.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1311,
"aa_ref": "R",
"aa_start": 545,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8350,
"cdna_start": 1773,
"cds_end": null,
"cds_length": 3936,
"cds_start": 1634,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047445581.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1634G>A",
"hgvs_p": "p.Arg545Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301537.1",
"strand": false,
"transcript": "XM_047445581.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1276,
"aa_ref": "R",
"aa_start": 495,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11866,
"cdna_start": 5244,
"cds_end": null,
"cds_length": 3831,
"cds_start": 1484,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011533064.3",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1484G>A",
"hgvs_p": "p.Arg495Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011531366.1",
"strand": false,
"transcript": "XM_011533064.3",
"transcript_support_level": null
},
{
"aa_alt": "K",
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"aa_length": 1276,
"aa_ref": "R",
"aa_start": 495,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8496,
"cdna_start": 1874,
"cds_end": null,
"cds_length": 3831,
"cds_start": 1484,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047445582.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1484G>A",
"hgvs_p": "p.Arg495Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301538.1",
"strand": false,
"transcript": "XM_047445582.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1187,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7951,
"cdna_start": 2284,
"cds_end": null,
"cds_length": 3564,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047445583.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301539.1",
"strand": false,
"transcript": "XM_047445583.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 1172,
"aa_ref": "R",
"aa_start": 552,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7906,
"cdna_start": 2284,
"cds_end": null,
"cds_length": 3519,
"cds_start": 1655,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047445584.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.1655G>A",
"hgvs_p": "p.Arg552Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301540.1",
"strand": false,
"transcript": "XM_047445584.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 978,
"aa_ref": "R",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7227,
"cdna_start": 605,
"cds_end": null,
"cds_length": 2937,
"cds_start": 590,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047445585.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "c.590G>A",
"hgvs_p": "p.Arg197Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301541.1",
"strand": false,
"transcript": "XM_047445585.1",
"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": 4370,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000472480.2",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "n.1535G>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": "ENST00000472480.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4898,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000688043.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "n.1876G>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": "ENST00000688043.1",
"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": 3407,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000689668.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "n.1662G>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": "ENST00000689668.1",
"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": 5987,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000690876.1",
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
"hgvs_c": "n.1544G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000508955.1",
"strand": false,
"transcript": "ENST00000690876.1",
"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": 4772,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000692620.1",
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"gene_symbol": "SOS1",
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"intron_rank": null,
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"mane_plus": null,
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"protein_coding": false,
"protein_id": "ENSP00000509311.1",
"strand": false,
"transcript": "ENST00000692620.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
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"dbscsnv_ada_score": null,
"dbsnp": "rs397517154",
"effect": "missense_variant",
"frequency_reference_population": 6.84192e-7,
"gene_hgnc_id": 11187,
"gene_symbol": "SOS1",
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"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Noonan syndrome|not provided|Noonan syndrome 3|Noonan syndrome 1|RASopathy|Noonan syndrome 4|Fibromatosis, gingival, 1",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.798,
"pos": 39022773,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.837,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005633.4"
}
]
}