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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: 9-131513305-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131513305&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131513305,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000402686.8",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His",
"transcript": "NM_001077365.2",
"protein_id": "NP_001070833.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 725,
"cds_start": 1149,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1335,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "ENST00000402686.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His",
"transcript": "ENST00000402686.8",
"protein_id": "ENSP00000385797.4",
"transcript_support_level": 1,
"aa_start": 383,
"aa_end": null,
"aa_length": 725,
"cds_start": 1149,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1335,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "NM_001077365.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1215C>T",
"hgvs_p": "p.His405His",
"transcript": "ENST00000372228.9",
"protein_id": "ENSP00000361302.3",
"transcript_support_level": 1,
"aa_start": 405,
"aa_end": null,
"aa_length": 747,
"cds_start": 1215,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1530,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1206C>T",
"hgvs_p": "p.His402His",
"transcript": "ENST00000423007.6",
"protein_id": "ENSP00000404119.2",
"transcript_support_level": 1,
"aa_start": 402,
"aa_end": null,
"aa_length": 744,
"cds_start": 1206,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 2235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1215C>T",
"hgvs_p": "p.His405His",
"transcript": "NM_001353193.2",
"protein_id": "NP_001340122.2",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 747,
"cds_start": 1215,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1641,
"cdna_end": null,
"cdna_length": 3363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1215C>T",
"hgvs_p": "p.His405His",
"transcript": "NM_007171.4",
"protein_id": "NP_009102.4",
"transcript_support_level": null,
"aa_start": 405,
"aa_end": null,
"aa_length": 747,
"cds_start": 1215,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 1401,
"cdna_end": null,
"cdna_length": 3123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His",
"transcript": "NM_001136113.2",
"protein_id": "NP_001129585.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 725,
"cds_start": 1149,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1575,
"cdna_end": null,
"cdna_length": 3297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His",
"transcript": "ENST00000676640.1",
"protein_id": "ENSP00000503281.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 725,
"cds_start": 1149,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 1587,
"cdna_end": null,
"cdna_length": 3309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1137C>T",
"hgvs_p": "p.His379His",
"transcript": "NM_001374689.1",
"protein_id": "NP_001361618.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 721,
"cds_start": 1137,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 3055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1059C>T",
"hgvs_p": "p.His353His",
"transcript": "NM_001353196.2",
"protein_id": "NP_001340125.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 695,
"cds_start": 1059,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1245,
"cdna_end": null,
"cdna_length": 2967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1059C>T",
"hgvs_p": "p.His353His",
"transcript": "ENST00000678303.1",
"protein_id": "ENSP00000503696.1",
"transcript_support_level": null,
"aa_start": 353,
"aa_end": null,
"aa_length": 695,
"cds_start": 1059,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1215,
"cdna_end": null,
"cdna_length": 2573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1053C>T",
"hgvs_p": "p.His351His",
"transcript": "NM_001353197.2",
"protein_id": "NP_001340126.2",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 693,
"cds_start": 1053,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 1249,
"cdna_end": null,
"cdna_length": 2971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1053C>T",
"hgvs_p": "p.His351His",
"transcript": "NM_001353198.2",
"protein_id": "NP_001340127.2",
"transcript_support_level": null,
"aa_start": 351,
"aa_end": null,
"aa_length": 693,
"cds_start": 1053,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 1950,
"cdna_end": null,
"cdna_length": 3672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.987C>T",
"hgvs_p": "p.His329His",
"transcript": "NM_001077366.2",
"protein_id": "NP_001070834.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 671,
"cds_start": 987,
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"cds_length": 2016,
"cdna_start": 1183,
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"cdna_length": 2905,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.987C>T",
"hgvs_p": "p.His329His",
"transcript": "NM_001353194.2",
"protein_id": "NP_001340123.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 671,
"cds_start": 987,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 1423,
"cdna_end": null,
"cdna_length": 3145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.987C>T",
"hgvs_p": "p.His329His",
"transcript": "ENST00000341012.13",
"protein_id": "ENSP00000343034.7",
"transcript_support_level": 2,
"aa_start": 329,
"aa_end": null,
"aa_length": 671,
"cds_start": 987,
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"cdna_start": 1206,
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"cdna_length": 2935,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His",
"transcript": "NM_001374690.1",
"protein_id": "NP_001361619.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 652,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 1335,
"cdna_end": null,
"cdna_length": 2838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.864C>T",
"hgvs_p": "p.His288His",
"transcript": "NM_001353199.2",
"protein_id": "NP_001340128.2",
"transcript_support_level": null,
"aa_start": 288,
"aa_end": null,
"aa_length": 630,
"cds_start": 864,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1142,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.798C>T",
"hgvs_p": "p.His266His",
"transcript": "NM_001136114.2",
"protein_id": "NP_001129586.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
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"cds_start": 798,
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"mane_select": null,
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"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.798C>T",
"hgvs_p": "p.His266His",
"transcript": "NM_001353195.2",
"protein_id": "NP_001340124.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
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"cds_start": 798,
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"cdna_start": 1228,
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"mane_select": null,
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"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.798C>T",
"hgvs_p": "p.His266His",
"transcript": "NM_001374691.1",
"protein_id": "NP_001361620.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 608,
"cds_start": 798,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1265,
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"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.798C>T",
"hgvs_p": "p.His266His",
"transcript": "NM_001374692.1",
"protein_id": "NP_001361621.1",
"transcript_support_level": null,
"aa_start": 266,
"aa_end": null,
"aa_length": 608,
"cds_start": 798,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1177,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
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"protein_id": "NP_001361622.1",
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},
{
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],
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"gene_symbol": "POMT1",
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},
{
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"gene_symbol": "POMT1",
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"transcript": "ENST00000678733.1",
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},
{
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"downstream_gene_variant"
],
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"gene_symbol": "POMT1",
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"hgvs_c": "n.*702C>T",
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"transcript": "ENST00000678942.2",
"protein_id": "ENSP00000504690.2",
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"cdna_length": 1244,
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"feature": null
}
],
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"dbsnp": "rs202121299",
"frequency_reference_population": 0.0003857106,
"hom_count_reference_population": 5,
"allele_count_reference_population": 622,
"gnomad_exomes_af": 0.000403989,
"gnomad_genomes_af": 0.000210288,
"gnomad_exomes_ac": 590,
"gnomad_genomes_ac": 32,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4000000059604645,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.887,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000402686.8",
"gene_symbol": "POMT1",
"hgnc_id": 9202,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.His383His"
}
],
"clinvar_disease": " type B1,Autosomal recessive limb-girdle muscular dystrophy type 2K,Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability),POMT1-related disorder,Walker-Warburg congenital muscular dystrophy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3 B:2",
"phenotype_combined": "not specified|not provided|Walker-Warburg congenital muscular dystrophy;Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1;Autosomal recessive limb-girdle muscular dystrophy type 2K|POMT1-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}