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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: 5-140691253-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=140691253&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 140691253,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000504156.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_002109.6",
"protein_id": "NP_002100.2",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 509,
"cds_start": 52,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 1948,
"mane_select": "ENST00000504156.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000504156.7",
"protein_id": "ENSP00000425634.1",
"transcript_support_level": 1,
"aa_start": 18,
"aa_end": null,
"aa_length": 509,
"cds_start": 52,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 1948,
"mane_select": "NM_002109.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000457527.6",
"protein_id": "ENSP00000387893.2",
"transcript_support_level": 1,
"aa_start": 18,
"aa_end": null,
"aa_length": 489,
"cds_start": 52,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 125,
"cdna_end": null,
"cdna_length": 1896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000507746.7",
"protein_id": "ENSP00000425889.2",
"transcript_support_level": 5,
"aa_start": 18,
"aa_end": null,
"aa_length": 512,
"cds_start": 52,
"cds_end": null,
"cds_length": 1539,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 1902,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000675204.1",
"protein_id": "ENSP00000501643.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 511,
"cds_start": 52,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 2327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_001258041.3",
"protein_id": "NP_001244970.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 489,
"cds_start": 52,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 1888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000676327.1",
"protein_id": "ENSP00000502594.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 473,
"cds_start": 52,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 137,
"cdna_end": null,
"cdna_length": 2729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000675366.1",
"protein_id": "ENSP00000501747.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 470,
"cds_start": 52,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 163,
"cdna_end": null,
"cdna_length": 2746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_001258040.3",
"protein_id": "NP_001244969.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 469,
"cds_start": 52,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 1828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000438307.6",
"protein_id": "ENSP00000411511.2",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 469,
"cds_start": 52,
"cds_end": null,
"cds_length": 1410,
"cdna_start": 89,
"cdna_end": null,
"cdna_length": 1789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_001258042.3",
"protein_id": "NP_001244971.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 449,
"cds_start": 52,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 118,
"cdna_end": null,
"cdna_length": 1768,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000307633.7",
"protein_id": "ENSP00000304668.3",
"transcript_support_level": 2,
"aa_start": 18,
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"aa_length": 449,
"cds_start": 52,
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"cds_length": 1350,
"cdna_start": 131,
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"cdna_length": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_001289092.2",
"protein_id": "NP_001276021.1",
"transcript_support_level": null,
"aa_start": 18,
"aa_end": null,
"aa_length": 435,
"cds_start": 52,
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"cds_length": 1308,
"cdna_start": 118,
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"cdna_length": 1726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 1,
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"exon_count": 11,
"intron_rank": null,
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"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000415192.6",
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},
{
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],
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "HARS1",
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"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000675851.1",
"protein_id": "ENSP00000502624.1",
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"aa_start": 18,
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"cds_start": 52,
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"cdna_start": 137,
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"cdna_length": 2507,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 1,
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"exon_count": 10,
"intron_rank": null,
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"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "NM_001289093.2",
"protein_id": "NP_001276022.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 1,
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"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000431330.7",
"protein_id": "ENSP00000393244.2",
"transcript_support_level": 2,
"aa_start": 18,
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"aa_length": 395,
"cds_start": 52,
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"cdna_length": 2643,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "V",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met",
"transcript": "ENST00000509087.2",
"protein_id": "ENSP00000502781.1",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 171,
"cds_start": 52,
"cds_end": null,
"cds_length": 516,
"cdna_start": 101,
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"cdna_length": 915,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.101G>A",
"hgvs_p": null,
"transcript": "ENST00000502888.2",
"protein_id": null,
"transcript_support_level": 2,
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},
{
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"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.137G>A",
"hgvs_p": null,
"transcript": "ENST00000506579.6",
"protein_id": null,
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"aa_start": null,
"aa_end": null,
"aa_length": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.52G>A",
"hgvs_p": null,
"transcript": "ENST00000512396.6",
"protein_id": "ENSP00000421576.1",
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"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": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.91G>A",
"hgvs_p": null,
"transcript": "ENST00000518126.6",
"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": 1145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.52G>A",
"hgvs_p": null,
"transcript": "ENST00000643686.1",
"protein_id": "ENSP00000493611.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS2",
"gene_hgnc_id": 4817,
"hgvs_c": "n.-231C>T",
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"transcript": "ENST00000511913.6",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 641,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS2",
"gene_hgnc_id": 4817,
"hgvs_c": "n.-305C>T",
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"transcript": "ENST00000520095.6",
"protein_id": "ENSP00000429220.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 1747,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"hgvs_c": "n.-18G>A",
"hgvs_p": null,
"transcript": "ENST00000646229.1",
"protein_id": "ENSP00000495358.1",
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"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": 1906,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
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"intron_rank_end": null,
"gene_symbol": "HARS2",
"gene_hgnc_id": 4817,
"hgvs_c": "n.-383C>T",
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"transcript": "ENST00000647484.1",
"protein_id": "ENSP00000494140.1",
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"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": 2310,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HARS1",
"gene_hgnc_id": 4816,
"dbsnp": "rs774632798",
"frequency_reference_population": 0.00005470922,
"hom_count_reference_population": 0,
"allele_count_reference_population": 88,
"gnomad_exomes_af": 0.0000542414,
"gnomad_genomes_af": 0.0000591903,
"gnomad_exomes_ac": 79,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5605599284172058,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.314,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9506,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.07,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.076,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000504156.7",
"gene_symbol": "HARS1",
"hgnc_id": 4816,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.52G>A",
"hgvs_p": "p.Val18Met"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000230771.9",
"gene_symbol": "HARS2",
"hgnc_id": 4817,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-396C>T",
"hgvs_p": null
}
],
"clinvar_disease": "HARS1-related disorder,Usher syndrome type 3B,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Usher syndrome type 3B|not specified|HARS1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}