chr20-5950269-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015939.5(TRMT6):c.128+9G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00669 in 1,597,026 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0055 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0068 ( 54 hom. )
Consequence
TRMT6
NM_015939.5 intron
NM_015939.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.118
Genes affected
TRMT6 (HGNC:20900): (tRNA methyltransferase 6 non-catalytic subunit) This gene encodes a member of the tRNA methyltransferase 6 protein family. A similar protein in yeast is part of a two component methyltransferase, which is involved in the posttranslational modification that produces the modified nucleoside 1-methyladenosine in tRNAs. Modified 1-methyladenosine influences initiator methionine stability and may be involved in the replication of human immunodeficiency virus type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 20-5950269-C-G is Benign according to our data. Variant chr20-5950269-C-G is described in ClinVar as [Benign]. Clinvar id is 770666.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00681 (9841/1444706) while in subpopulation AMR AF= 0.021 (921/43916). AF 95% confidence interval is 0.0198. There are 54 homozygotes in gnomad4_exome. There are 4756 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRMT6 | NM_015939.5 | c.128+9G>C | intron_variant | ENST00000203001.7 | |||
TRMT6 | NM_001281467.2 | c.-273+9G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT6 | ENST00000203001.7 | c.128+9G>C | intron_variant | 1 | NM_015939.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00553 AC: 841AN: 152202Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00780 AC: 1891AN: 242402Hom.: 19 AF XY: 0.00715 AC XY: 940AN XY: 131464
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GnomAD4 exome AF: 0.00681 AC: 9841AN: 1444706Hom.: 54 Cov.: 31 AF XY: 0.00664 AC XY: 4756AN XY: 716558
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GnomAD4 genome ? AF: 0.00551 AC: 839AN: 152320Hom.: 6 Cov.: 32 AF XY: 0.00575 AC XY: 428AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at