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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: 1-32781140-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=32781140&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 32781140,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003680.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1048A>G",
"hgvs_p": "p.Met350Val",
"transcript": "NM_003680.4",
"protein_id": "NP_003671.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 528,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373477.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003680.4"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1048A>G",
"hgvs_p": "p.Met350Val",
"transcript": "ENST00000373477.9",
"protein_id": "ENSP00000362576.4",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 528,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003680.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373477.9"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1135A>G",
"hgvs_p": "p.Met379Val",
"transcript": "ENST00000906066.1",
"protein_id": "ENSP00000576125.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 557,
"cds_start": 1135,
"cds_end": null,
"cds_length": 1674,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906066.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Met349Val",
"transcript": "ENST00000918766.1",
"protein_id": "ENSP00000588825.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 527,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918766.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1045A>G",
"hgvs_p": "p.Met349Val",
"transcript": "ENST00000918768.1",
"protein_id": "ENSP00000588827.1",
"transcript_support_level": null,
"aa_start": 349,
"aa_end": null,
"aa_length": 527,
"cds_start": 1045,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918768.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1048A>G",
"hgvs_p": "p.Met350Val",
"transcript": "ENST00000956435.1",
"protein_id": "ENSP00000626494.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 524,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000956435.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.1048A>G",
"hgvs_p": "p.Met350Val",
"transcript": "ENST00000906068.1",
"protein_id": "ENSP00000576127.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 506,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906068.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.967A>G",
"hgvs_p": "p.Met323Val",
"transcript": "ENST00000906065.1",
"protein_id": "ENSP00000576124.1",
"transcript_support_level": null,
"aa_start": 323,
"aa_end": null,
"aa_length": 501,
"cds_start": 967,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906065.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.955A>G",
"hgvs_p": "p.Met319Val",
"transcript": "ENST00000918767.1",
"protein_id": "ENSP00000588826.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 497,
"cds_start": 955,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918767.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.901A>G",
"hgvs_p": "p.Met301Val",
"transcript": "ENST00000675785.2",
"protein_id": "ENSP00000502019.1",
"transcript_support_level": null,
"aa_start": 301,
"aa_end": null,
"aa_length": 479,
"cds_start": 901,
"cds_end": null,
"cds_length": 1440,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675785.2"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.874A>G",
"hgvs_p": "p.Met292Val",
"transcript": "ENST00000906067.1",
"protein_id": "ENSP00000576126.1",
"transcript_support_level": null,
"aa_start": 292,
"aa_end": null,
"aa_length": 470,
"cds_start": 874,
"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": "ENST00000906067.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.826A>G",
"hgvs_p": "p.Met276Val",
"transcript": "ENST00000906064.1",
"protein_id": "ENSP00000576123.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 454,
"cds_start": 826,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906064.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.733A>G",
"hgvs_p": "p.Met245Val",
"transcript": "ENST00000918770.1",
"protein_id": "ENSP00000588829.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 423,
"cds_start": 733,
"cds_end": null,
"cds_length": 1272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918770.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.652A>G",
"hgvs_p": "p.Met218Val",
"transcript": "ENST00000918769.1",
"protein_id": "ENSP00000588828.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 396,
"cds_start": 652,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918769.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.595A>G",
"hgvs_p": "p.Met199Val",
"transcript": "ENST00000906069.1",
"protein_id": "ENSP00000576128.1",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 377,
"cds_start": 595,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000906069.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "c.418A>G",
"hgvs_p": "p.Met140Val",
"transcript": "XM_011542347.3",
"protein_id": "XP_011540649.1",
"transcript_support_level": null,
"aa_start": 140,
"aa_end": null,
"aa_length": 318,
"cds_start": 418,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011542347.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.964A>G",
"hgvs_p": null,
"transcript": "ENST00000469100.5",
"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": "ENST00000469100.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.515A>G",
"hgvs_p": null,
"transcript": "ENST00000478828.1",
"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": "ENST00000478828.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.1358A>G",
"hgvs_p": null,
"transcript": "ENST00000487404.5",
"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": "ENST00000487404.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.*596A>G",
"hgvs_p": null,
"transcript": "ENST00000674629.1",
"protein_id": "ENSP00000502470.1",
"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": "ENST00000674629.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.*1008A>G",
"hgvs_p": null,
"transcript": "ENST00000674654.1",
"protein_id": "ENSP00000501729.1",
"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": "ENST00000674654.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"hgvs_c": "n.*1222A>G",
"hgvs_p": null,
"transcript": "ENST00000676297.1",
"protein_id": "ENSP00000501596.1",
"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": "ENST00000676297.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
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"exon_count": 11,
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"transcript": "ENST00000674629.1",
"protein_id": "ENSP00000502470.1",
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{
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"canonical": false,
"protein_coding": false,
"strand": false,
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"3_prime_UTR_variant"
],
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"gene_symbol": "YARS1",
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"hgvs_c": "n.*1008A>G",
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"transcript": "ENST00000674654.1",
"protein_id": "ENSP00000501729.1",
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"cdna_start": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000674654.1"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
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"exon_count": 13,
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"gene_symbol": "YARS1",
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"hgvs_c": "n.*1222A>G",
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"transcript": "ENST00000676297.1",
"protein_id": "ENSP00000501596.1",
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"aa_length": null,
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"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": null,
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"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000676297.1"
}
],
"gene_symbol": "YARS1",
"gene_hgnc_id": 12840,
"dbsnp": "rs1553122785",
"frequency_reference_population": 0.0000054729444,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000547294,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.031246691942214966,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.15000000596046448,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.065,
"revel_prediction": "Benign",
"alphamissense_score": 0.046,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.64,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.174,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.15,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_003680.4",
"gene_symbol": "YARS1",
"hgnc_id": 12840,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1048A>G",
"hgvs_p": "p.Met350Val"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease dominant intermediate C",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Charcot-Marie-Tooth disease dominant intermediate C",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}