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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: X-40591350-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=40591350&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 40591350,
"ref": "G",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000636580.2",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "NM_005765.3",
"protein_id": "NP_005756.2",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 350,
"cds_start": 285,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 2242,
"mane_select": "ENST00000636580.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000636580.2",
"protein_id": "ENSP00000490083.1",
"transcript_support_level": 1,
"aa_start": 95,
"aa_end": null,
"aa_length": 350,
"cds_start": 285,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 2242,
"mane_select": "NM_005765.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.285G>C",
"hgvs_p": null,
"transcript": "ENST00000636639.1",
"protein_id": "ENSP00000490382.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000378438.9",
"protein_id": "ENSP00000367697.5",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 349,
"cds_start": 285,
"cds_end": null,
"cds_length": 1050,
"cdna_start": 393,
"cdna_end": null,
"cdna_length": 2022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000636196.1",
"protein_id": "ENSP00000490675.1",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 345,
"cds_start": 285,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 1403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000638153.1",
"protein_id": "ENSP00000490239.1",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 331,
"cds_start": 285,
"cds_end": null,
"cds_length": 996,
"cdna_start": 402,
"cdna_end": null,
"cdna_length": 1303,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000636409.1",
"protein_id": "ENSP00000489819.1",
"transcript_support_level": 2,
"aa_start": 95,
"aa_end": null,
"aa_length": 318,
"cds_start": 285,
"cds_end": null,
"cds_length": 957,
"cdna_start": 457,
"cdna_end": null,
"cdna_length": 1962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000636287.1",
"protein_id": "ENSP00000490452.1",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 317,
"cds_start": 285,
"cds_end": null,
"cds_length": 954,
"cdna_start": 353,
"cdna_end": null,
"cdna_length": 1904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.138G>C",
"hgvs_p": "p.Ser46Ser",
"transcript": "ENST00000637526.1",
"protein_id": "ENSP00000489845.1",
"transcript_support_level": 5,
"aa_start": 46,
"aa_end": null,
"aa_length": 301,
"cds_start": 138,
"cds_end": null,
"cds_length": 906,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 1862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.234G>C",
"hgvs_p": "p.Ser78Ser",
"transcript": "ENST00000637955.1",
"protein_id": "ENSP00000489622.1",
"transcript_support_level": 5,
"aa_start": 78,
"aa_end": null,
"aa_length": 293,
"cds_start": 234,
"cds_end": null,
"cds_length": 882,
"cdna_start": 236,
"cdna_end": null,
"cdna_length": 1084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.57G>C",
"hgvs_p": "p.Ser19Ser",
"transcript": "ENST00000637327.1",
"protein_id": "ENSP00000490558.1",
"transcript_support_level": 2,
"aa_start": 19,
"aa_end": null,
"aa_length": 274,
"cds_start": 57,
"cds_end": null,
"cds_length": 825,
"cdna_start": 310,
"cdna_end": null,
"cdna_length": 1929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.57G>C",
"hgvs_p": "p.Ser19Ser",
"transcript": "ENST00000636251.1",
"protein_id": "ENSP00000489920.1",
"transcript_support_level": 5,
"aa_start": 19,
"aa_end": null,
"aa_length": 273,
"cds_start": 57,
"cds_end": null,
"cds_length": 822,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 1877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000423649.2",
"protein_id": "ENSP00000410105.2",
"transcript_support_level": 2,
"aa_start": 95,
"aa_end": null,
"aa_length": 272,
"cds_start": 285,
"cds_end": null,
"cds_length": 819,
"cdna_start": 369,
"cdna_end": null,
"cdna_length": 1093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser",
"transcript": "ENST00000447485.6",
"protein_id": "ENSP00000411317.2",
"transcript_support_level": 5,
"aa_start": 95,
"aa_end": null,
"aa_length": 262,
"cds_start": 285,
"cds_end": null,
"cds_length": 789,
"cdna_start": 315,
"cdna_end": null,
"cdna_length": 1254,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.57G>C",
"hgvs_p": "p.Ser19Ser",
"transcript": "ENST00000636970.1",
"protein_id": "ENSP00000490462.1",
"transcript_support_level": 5,
"aa_start": 19,
"aa_end": null,
"aa_length": 242,
"cds_start": 57,
"cds_end": null,
"cds_length": 729,
"cdna_start": 260,
"cdna_end": null,
"cdna_length": 1187,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.57G>C",
"hgvs_p": "p.Ser19Ser",
"transcript": "ENST00000637482.1",
"protein_id": "ENSP00000490532.1",
"transcript_support_level": 5,
"aa_start": 19,
"aa_end": null,
"aa_length": 196,
"cds_start": 57,
"cds_end": null,
"cds_length": 591,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 1648,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.81G>C",
"hgvs_p": "p.Ser27Ser",
"transcript": "ENST00000637614.1",
"protein_id": "ENSP00000490884.1",
"transcript_support_level": 5,
"aa_start": 27,
"aa_end": null,
"aa_length": 186,
"cds_start": 81,
"cds_end": null,
"cds_length": 561,
"cdna_start": 81,
"cdna_end": null,
"cdna_length": 621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "c.138G>C",
"hgvs_p": "p.Ser46Ser",
"transcript": "ENST00000436783.6",
"protein_id": "ENSP00000403969.2",
"transcript_support_level": 5,
"aa_start": 46,
"aa_end": null,
"aa_length": 127,
"cds_start": 138,
"cds_end": null,
"cds_length": 384,
"cdna_start": 308,
"cdna_end": null,
"cdna_length": 554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.57G>C",
"hgvs_p": null,
"transcript": "ENST00000486558.6",
"protein_id": "ENSP00000490706.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 832,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.451G>C",
"hgvs_p": null,
"transcript": "ENST00000487051.2",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.57G>C",
"hgvs_p": null,
"transcript": "ENST00000635734.1",
"protein_id": "ENSP00000489653.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1851,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.285G>C",
"hgvs_p": null,
"transcript": "ENST00000635774.1",
"protein_id": "ENSP00000490733.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1995,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.92G>C",
"hgvs_p": null,
"transcript": "ENST00000635829.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
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"non_coding_transcript_exon_variant"
],
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
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"exon_count": 9,
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"gene_symbol": "ATP6AP2",
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"hgvs_c": "n.285G>C",
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"transcript": "ENST00000636787.1",
"protein_id": "ENSP00000490954.1",
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"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
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"exon_count": 2,
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"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"hgvs_c": "n.2473G>C",
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"transcript": "ENST00000637954.1",
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"transcript_support_level": 2,
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"aa_length": null,
"cds_start": -4,
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"cdna_length": 3593,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP6AP2",
"gene_hgnc_id": 18305,
"dbsnp": "rs34217273",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0.00000182288,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09300000220537186,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.093,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.88,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2.904,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000636580.2",
"gene_symbol": "ATP6AP2",
"hgnc_id": 18305,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AR,Unknown",
"hgvs_c": "c.285G>C",
"hgvs_p": "p.Ser95Ser"
}
],
"clinvar_disease": "Syndromic X-linked intellectual disability Hedera type",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Syndromic X-linked intellectual disability Hedera type",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}