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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: 4-76179654-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=76179654&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 76179654,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005506.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "NM_005506.4",
"protein_id": "NP_005497.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 478,
"cds_start": 475,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264896.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005506.4"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000264896.8",
"protein_id": "ENSP00000264896.2",
"transcript_support_level": 1,
"aa_start": 159,
"aa_end": null,
"aa_length": 478,
"cds_start": 475,
"cds_end": null,
"cds_length": 1437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005506.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264896.8"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000638295.1",
"protein_id": "ENSP00000492288.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 320,
"cds_start": 1,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638295.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047416429.1",
"protein_id": "XP_047272385.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 320,
"cds_start": 1,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416429.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047416430.1",
"protein_id": "XP_047272386.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 320,
"cds_start": 1,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416430.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.595A>G",
"hgvs_p": "p.Met199Val",
"transcript": "ENST00000640634.1",
"protein_id": "ENSP00000492737.1",
"transcript_support_level": 5,
"aa_start": 199,
"aa_end": null,
"aa_length": 518,
"cds_start": 595,
"cds_end": null,
"cds_length": 1557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640634.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000862445.1",
"protein_id": "ENSP00000532504.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 486,
"cds_start": 475,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862445.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.466A>G",
"hgvs_p": "p.Met156Val",
"transcript": "ENST00000639145.1",
"protein_id": "ENSP00000492831.1",
"transcript_support_level": 5,
"aa_start": 156,
"aa_end": null,
"aa_length": 475,
"cds_start": 466,
"cds_end": null,
"cds_length": 1428,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639145.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000862444.1",
"protein_id": "ENSP00000532503.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 471,
"cds_start": 475,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862444.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000640957.1",
"protein_id": "ENSP00000492004.1",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 470,
"cds_start": 475,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640957.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000862443.1",
"protein_id": "ENSP00000532502.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 464,
"cds_start": 475,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862443.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000640640.1",
"protein_id": "ENSP00000492246.1",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 449,
"cds_start": 475,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640640.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000638603.1",
"protein_id": "ENSP00000491728.1",
"transcript_support_level": 5,
"aa_start": 159,
"aa_end": null,
"aa_length": 438,
"cds_start": 475,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638603.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val",
"transcript": "ENST00000921155.1",
"protein_id": "ENSP00000591214.1",
"transcript_support_level": null,
"aa_start": 159,
"aa_end": null,
"aa_length": 436,
"cds_start": 475,
"cds_end": null,
"cds_length": 1311,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921155.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.423+1300A>G",
"hgvs_p": null,
"transcript": "ENST00000862442.1",
"protein_id": "ENSP00000532501.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 415,
"cds_start": null,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862442.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.276-3744A>G",
"hgvs_p": null,
"transcript": "NM_001204255.2",
"protein_id": "NP_001191184.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001204255.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.276-3744A>G",
"hgvs_p": null,
"transcript": "ENST00000452464.6",
"protein_id": "ENSP00000399154.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 335,
"cds_start": null,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452464.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "c.276-13353A>G",
"hgvs_p": null,
"transcript": "ENST00000639738.1",
"protein_id": "ENSP00000491792.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": null,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639738.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "n.1976A>G",
"hgvs_p": null,
"transcript": "ENST00000502908.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000502908.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "n.727A>G",
"hgvs_p": null,
"transcript": "ENST00000638372.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000638372.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "n.475A>G",
"hgvs_p": null,
"transcript": "ENST00000638663.1",
"protein_id": "ENSP00000491407.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000638663.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARB2",
"gene_hgnc_id": 1665,
"hgvs_c": "n.2056A>G",
"hgvs_p": null,
"transcript": "ENST00000638680.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000638680.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
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{
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{
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],
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"dbsnp": "rs143655258",
"frequency_reference_population": 0.009236692,
"hom_count_reference_population": 98,
"allele_count_reference_population": 14909,
"gnomad_exomes_af": 0.00932842,
"gnomad_genomes_af": 0.00835653,
"gnomad_exomes_ac": 13636,
"gnomad_genomes_ac": 1273,
"gnomad_exomes_homalt": 90,
"gnomad_genomes_homalt": 8,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007808804512023926,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.126,
"revel_prediction": "Benign",
"alphamissense_score": 0.0774,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.14,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005506.4",
"gene_symbol": "SCARB2",
"hgnc_id": 1665,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.475A>G",
"hgvs_p": "p.Met159Val"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000651366.1",
"gene_symbol": "ENSG00000286074",
"hgnc_id": 58820,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.103-20312T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Action myoclonus-renal failure syndrome,Focal segmental glomerulosclerosis,Inborn genetic diseases,Progressive myoclonic epilepsy,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Action myoclonus-renal failure syndrome|not provided|Progressive myoclonic epilepsy|Focal segmental glomerulosclerosis|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}