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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: 19-13105032-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=13105032&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 13105032,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_017722.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile",
"transcript": "NM_001136035.4",
"protein_id": "NP_001129507.1",
"transcript_support_level": null,
"aa_start": 628,
"aa_end": null,
"aa_length": 659,
"cds_start": 1883,
"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": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile",
"transcript": "ENST00000357720.9",
"protein_id": "ENSP00000350352.4",
"transcript_support_level": 2,
"aa_start": 628,
"aa_end": null,
"aa_length": 659,
"cds_start": 1883,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile",
"transcript": "ENST00000437766.5",
"protein_id": "ENSP00000416149.1",
"transcript_support_level": 1,
"aa_start": 628,
"aa_end": null,
"aa_length": 659,
"cds_start": 1883,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1796C>T",
"hgvs_p": "p.Thr599Ile",
"transcript": "ENST00000221504.12",
"protein_id": "ENSP00000221504.7",
"transcript_support_level": 1,
"aa_start": 599,
"aa_end": null,
"aa_length": 630,
"cds_start": 1796,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile",
"transcript": "NM_017722.5",
"protein_id": "NP_060192.1",
"transcript_support_level": null,
"aa_start": 628,
"aa_end": null,
"aa_length": 659,
"cds_start": 1883,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile",
"transcript": "ENST00000592062.5",
"protein_id": "ENSP00000466967.1",
"transcript_support_level": 5,
"aa_start": 628,
"aa_end": null,
"aa_length": 659,
"cds_start": 1883,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1880C>T",
"hgvs_p": "p.Thr627Ile",
"transcript": "ENST00000913623.1",
"protein_id": "ENSP00000583682.1",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 658,
"cds_start": 1880,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1880C>T",
"hgvs_p": "p.Thr627Ile",
"transcript": "ENST00000913624.1",
"protein_id": "ENSP00000583683.1",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 658,
"cds_start": 1880,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1859C>T",
"hgvs_p": "p.Thr620Ile",
"transcript": "ENST00000907296.1",
"protein_id": "ENSP00000577355.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 651,
"cds_start": 1859,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1817C>T",
"hgvs_p": "p.Thr606Ile",
"transcript": "ENST00000907297.1",
"protein_id": "ENSP00000577356.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 637,
"cds_start": 1817,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1796C>T",
"hgvs_p": "p.Thr599Ile",
"transcript": "NM_001142554.3",
"protein_id": "NP_001136026.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 630,
"cds_start": 1796,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1796C>T",
"hgvs_p": "p.Thr599Ile",
"transcript": "NM_001351760.2",
"protein_id": "NP_001338689.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 630,
"cds_start": 1796,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1796C>T",
"hgvs_p": "p.Thr599Ile",
"transcript": "ENST00000907294.1",
"protein_id": "ENSP00000577353.1",
"transcript_support_level": null,
"aa_start": 599,
"aa_end": null,
"aa_length": 630,
"cds_start": 1796,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1793C>T",
"hgvs_p": "p.Thr598Ile",
"transcript": "ENST00000913628.1",
"protein_id": "ENSP00000583687.1",
"transcript_support_level": null,
"aa_start": 598,
"aa_end": null,
"aa_length": 629,
"cds_start": 1793,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1775C>T",
"hgvs_p": "p.Thr592Ile",
"transcript": "NM_001351761.2",
"protein_id": "NP_001338690.1",
"transcript_support_level": null,
"aa_start": 592,
"aa_end": null,
"aa_length": 623,
"cds_start": 1775,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1772C>T",
"hgvs_p": "p.Thr591Ile",
"transcript": "ENST00000907295.1",
"protein_id": "ENSP00000577354.1",
"transcript_support_level": null,
"aa_start": 591,
"aa_end": null,
"aa_length": 622,
"cds_start": 1772,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1757C>T",
"hgvs_p": "p.Thr586Ile",
"transcript": "ENST00000913627.1",
"protein_id": "ENSP00000583686.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 617,
"cds_start": 1757,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1748C>T",
"hgvs_p": "p.Thr583Ile",
"transcript": "ENST00000907298.1",
"protein_id": "ENSP00000577357.1",
"transcript_support_level": null,
"aa_start": 583,
"aa_end": null,
"aa_length": 614,
"cds_start": 1748,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000907298.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1721C>T",
"hgvs_p": "p.Thr574Ile",
"transcript": "ENST00000913622.1",
"protein_id": "ENSP00000583681.1",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 605,
"cds_start": 1721,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1661C>T",
"hgvs_p": "p.Thr554Ile",
"transcript": "ENST00000960268.1",
"protein_id": "ENSP00000630327.1",
"transcript_support_level": null,
"aa_start": 554,
"aa_end": null,
"aa_length": 585,
"cds_start": 1661,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1589C>T",
"hgvs_p": "p.Thr530Ile",
"transcript": "ENST00000913625.1",
"protein_id": "ENSP00000583684.1",
"transcript_support_level": null,
"aa_start": 530,
"aa_end": null,
"aa_length": 561,
"cds_start": 1589,
"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": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1",
"gene_hgnc_id": 25980,
"hgvs_c": "c.1556C>T",
"hgvs_p": "p.Thr519Ile",
"transcript": "ENST00000913626.1",
"protein_id": "ENSP00000583685.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 550,
"cds_start": 1556,
"cds_end": null,
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"cdna_start": null,
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{
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{
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],
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{
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],
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"biotype": "retained_intron",
"feature": "ENST00000593157.5"
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
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],
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"biotype": "pseudogene",
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{
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"strand": true,
"consequences": [
"downstream_gene_variant"
],
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{
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],
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"gene_symbol": "LOC105372282",
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],
"gene_symbol": "TRMT1",
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"dbsnp": "rs577720271",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 90,
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"gnomad_genomes_af": 0.0000656435,
"gnomad_exomes_ac": 80,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008282184600830078,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.022,
"revel_prediction": "Benign",
"alphamissense_score": 0.0766,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.56,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.396,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS1"
],
"verdict": "Benign",
"transcript": "NM_017722.5",
"gene_symbol": "TRMT1",
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"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1883C>T",
"hgvs_p": "p.Thr628Ile"
},
{
"score": -6,
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"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000798943.1",
"gene_symbol": "ENSG00000304024",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.479+122G>A",
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},
{
"score": -6,
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"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "XR_001753871.2",
"gene_symbol": "LOC105372282",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*126G>A",
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}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}