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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: 9-87727613-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=87727613&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 87727613,
"ref": "A",
"alt": "G",
"effect": "5_prime_UTR_premature_start_codon_gain_variant",
"transcript": "NM_001257973.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "NM_001912.5",
"protein_id": "NP_001903.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000343150.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001912.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000343150.10",
"protein_id": "ENSP00000345344.5",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001912.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000343150.10"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000340342.11",
"protein_id": "ENSP00000365061.5",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000340342.11"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "n.119A>G",
"hgvs_p": null,
"transcript": "ENST00000495822.2",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000495822.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.-107A>G",
"hgvs_p": null,
"transcript": "NM_001257973.2",
"protein_id": "NP_001244902.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": null,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001257973.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000678596.1",
"protein_id": "ENSP00000503146.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 341,
"cds_start": 10,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678596.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000678649.1",
"protein_id": "ENSP00000504772.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 341,
"cds_start": 10,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678649.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "NM_001257971.2",
"protein_id": "NP_001244900.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001257971.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "NM_001257972.2",
"protein_id": "NP_001244901.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001257972.2"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "NM_001382757.1",
"protein_id": "NP_001369686.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001382757.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "NM_145918.3",
"protein_id": "NP_666023.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145918.3"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000676480.1",
"protein_id": "ENSP00000504279.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676480.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000676531.1",
"protein_id": "ENSP00000503439.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676531.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000676881.1",
"protein_id": "ENSP00000502901.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676881.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000676946.1",
"protein_id": "ENSP00000503470.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676946.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000677262.1",
"protein_id": "ENSP00000503851.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677262.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000677761.1",
"protein_id": "ENSP00000503938.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677761.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000677821.1",
"protein_id": "ENSP00000503298.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000677821.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000678442.1",
"protein_id": "ENSP00000503897.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678442.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000679149.1",
"protein_id": "ENSP00000504313.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679149.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000679157.1",
"protein_id": "ENSP00000502968.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679157.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "c.10A>G",
"hgvs_p": "p.Thr4Ala",
"transcript": "ENST00000882604.1",
"protein_id": "ENSP00000552663.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 333,
"cds_start": 10,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000882604.1"
},
{
"aa_ref": "T",
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"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": "ENST00000679025.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "n.10A>G",
"hgvs_p": null,
"transcript": "ENST00000679028.1",
"protein_id": "ENSP00000503119.1",
"transcript_support_level": null,
"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": "ENST00000679028.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "n.151A>G",
"hgvs_p": null,
"transcript": "ENST00000679141.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000679141.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"hgvs_c": "n.1401A>G",
"hgvs_p": null,
"transcript": "ENST00000679252.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000679252.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304058",
"gene_hgnc_id": null,
"hgvs_c": "n.46-4593T>C",
"hgvs_p": null,
"transcript": "ENST00000799159.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000799159.1"
}
],
"gene_symbol": "CTSL",
"gene_hgnc_id": 2537,
"dbsnp": "rs982050868",
"frequency_reference_population": 0.0000037175641,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000273623,
"gnomad_genomes_af": 0.0000131499,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05692094564437866,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.018,
"revel_prediction": "Benign",
"alphamissense_score": 0.0595,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.015,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001257973.2",
"gene_symbol": "CTSL",
"hgnc_id": 2537,
"effects": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-107A>G",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000799159.1",
"gene_symbol": "ENSG00000304058",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.46-4593T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}