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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: 19-13105267-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13105267&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13105267,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_017722.5",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu",
"transcript": "NM_001136035.4",
"protein_id": "NP_001129507.1",
"transcript_support_level": null,
"aa_start": 611,
"aa_end": null,
"aa_length": 659,
"cds_start": 1833,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357720.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001136035.4"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu",
"transcript": "ENST00000357720.9",
"protein_id": "ENSP00000350352.4",
"transcript_support_level": 2,
"aa_start": 611,
"aa_end": null,
"aa_length": 659,
"cds_start": 1833,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001136035.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357720.9"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu",
"transcript": "ENST00000437766.5",
"protein_id": "ENSP00000416149.1",
"transcript_support_level": 1,
"aa_start": 611,
"aa_end": null,
"aa_length": 659,
"cds_start": 1833,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000437766.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1746G>A",
"hgvs_p": "p.Glu582Glu",
"transcript": "ENST00000221504.12",
"protein_id": "ENSP00000221504.7",
"transcript_support_level": 1,
"aa_start": 582,
"aa_end": null,
"aa_length": 630,
"cds_start": 1746,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000221504.12"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu",
"transcript": "NM_017722.5",
"protein_id": "NP_060192.1",
"transcript_support_level": null,
"aa_start": 611,
"aa_end": null,
"aa_length": 659,
"cds_start": 1833,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017722.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu",
"transcript": "ENST00000592062.5",
"protein_id": "ENSP00000466967.1",
"transcript_support_level": 5,
"aa_start": 611,
"aa_end": null,
"aa_length": 659,
"cds_start": 1833,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592062.5"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1830G>A",
"hgvs_p": "p.Glu610Glu",
"transcript": "ENST00000913623.1",
"protein_id": "ENSP00000583682.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 658,
"cds_start": 1830,
"cds_end": null,
"cds_length": 1977,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913623.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1830G>A",
"hgvs_p": "p.Glu610Glu",
"transcript": "ENST00000913624.1",
"protein_id": "ENSP00000583683.1",
"transcript_support_level": null,
"aa_start": 610,
"aa_end": null,
"aa_length": 658,
"cds_start": 1830,
"cds_end": null,
"cds_length": 1977,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913624.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1809G>A",
"hgvs_p": "p.Glu603Glu",
"transcript": "ENST00000907296.1",
"protein_id": "ENSP00000577355.1",
"transcript_support_level": null,
"aa_start": 603,
"aa_end": null,
"aa_length": 651,
"cds_start": 1809,
"cds_end": null,
"cds_length": 1956,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907296.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1767G>A",
"hgvs_p": "p.Glu589Glu",
"transcript": "ENST00000907297.1",
"protein_id": "ENSP00000577356.1",
"transcript_support_level": null,
"aa_start": 589,
"aa_end": null,
"aa_length": 637,
"cds_start": 1767,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907297.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1746G>A",
"hgvs_p": "p.Glu582Glu",
"transcript": "NM_001142554.3",
"protein_id": "NP_001136026.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 630,
"cds_start": 1746,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142554.3"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1746G>A",
"hgvs_p": "p.Glu582Glu",
"transcript": "NM_001351760.2",
"protein_id": "NP_001338689.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 630,
"cds_start": 1746,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351760.2"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1746G>A",
"hgvs_p": "p.Glu582Glu",
"transcript": "ENST00000907294.1",
"protein_id": "ENSP00000577353.1",
"transcript_support_level": null,
"aa_start": 582,
"aa_end": null,
"aa_length": 630,
"cds_start": 1746,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907294.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1743G>A",
"hgvs_p": "p.Glu581Glu",
"transcript": "ENST00000913628.1",
"protein_id": "ENSP00000583687.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 629,
"cds_start": 1743,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913628.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Glu575Glu",
"transcript": "NM_001351761.2",
"protein_id": "NP_001338690.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 623,
"cds_start": 1725,
"cds_end": null,
"cds_length": 1872,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001351761.2"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1722G>A",
"hgvs_p": "p.Glu574Glu",
"transcript": "ENST00000907295.1",
"protein_id": "ENSP00000577354.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 622,
"cds_start": 1722,
"cds_end": null,
"cds_length": 1869,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907295.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1707G>A",
"hgvs_p": "p.Glu569Glu",
"transcript": "ENST00000913627.1",
"protein_id": "ENSP00000583686.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 617,
"cds_start": 1707,
"cds_end": null,
"cds_length": 1854,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913627.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1698G>A",
"hgvs_p": "p.Glu566Glu",
"transcript": "ENST00000907298.1",
"protein_id": "ENSP00000577357.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 614,
"cds_start": 1698,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907298.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1671G>A",
"hgvs_p": "p.Glu557Glu",
"transcript": "ENST00000913622.1",
"protein_id": "ENSP00000583681.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 605,
"cds_start": 1671,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913622.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1611G>A",
"hgvs_p": "p.Glu537Glu",
"transcript": "ENST00000960268.1",
"protein_id": "ENSP00000630327.1",
"transcript_support_level": null,
"aa_start": 537,
"aa_end": null,
"aa_length": 585,
"cds_start": 1611,
"cds_end": null,
"cds_length": 1758,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960268.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1539G>A",
"hgvs_p": "p.Glu513Glu",
"transcript": "ENST00000913625.1",
"protein_id": "ENSP00000583684.1",
"transcript_support_level": null,
"aa_start": 513,
"aa_end": null,
"aa_length": 561,
"cds_start": 1539,
"cds_end": null,
"cds_length": 1686,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913625.1"
},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
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"protein_id": "ENSP00000583685.1",
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"aa_start": 502,
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"biotype": "protein_coding",
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},
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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"synonymous_variant"
],
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"exon_count": 16,
"intron_rank": null,
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"gene_symbol": "TRMT1",
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"hgvs_c": "c.1050G>A",
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"transcript": "NM_001351762.2",
"protein_id": "NP_001338691.1",
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"aa_start": 350,
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"aa_length": 398,
"cds_start": 1050,
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"biotype": "protein_coding",
"feature": "NM_001351762.2"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
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"exon_count": 15,
"intron_rank": null,
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"gene_symbol": "TRMT1",
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"hgvs_c": "n.2108G>A",
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"transcript": "ENST00000588511.5",
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"transcript_support_level": 5,
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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": "retained_intron",
"feature": "ENST00000588511.5"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
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"exon_count": 16,
"intron_rank": null,
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"gene_symbol": "TRMT1",
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"hgvs_c": "n.1952G>A",
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"transcript": "ENST00000593157.5",
"protein_id": null,
"transcript_support_level": 2,
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"aa_length": null,
"cds_start": null,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000593157.5"
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 3,
"intron_rank": 2,
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"gene_symbol": "ENSG00000304024",
"gene_hgnc_id": null,
"hgvs_c": "n.479+357C>T",
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"transcript": "ENST00000798943.1",
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"transcript_support_level": null,
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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": "pseudogene",
"feature": "ENST00000798943.1"
}
],
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"dbsnp": "rs778368877",
"frequency_reference_population": 0.0000899304,
"hom_count_reference_population": 0,
"allele_count_reference_population": 145,
"gnomad_exomes_af": 0.000096565,
"gnomad_genomes_af": 0.0000262809,
"gnomad_exomes_ac": 141,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9679999947547913,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.712,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.34,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.997016985938321,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_017722.5",
"gene_symbol": "TRMT1",
"hgnc_id": 25980,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1833G>A",
"hgvs_p": "p.Glu611Glu"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000798943.1",
"gene_symbol": "ENSG00000304024",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.479+357C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 68,Intellectual developmental disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Intellectual developmental disorder, autosomal recessive 68",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}