13-113799401-C-T
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_182614.4(TMEM255B):c.405C>T(p.Tyr135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00104 in 1,614,162 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00063 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 1 hom. )
Consequence
TMEM255B
NM_182614.4 synonymous
NM_182614.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.835
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 13-113799401-C-T is Benign according to our data. Variant chr13-113799401-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644015.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.835 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM255B | NM_182614.4 | c.405C>T | p.Tyr135= | synonymous_variant | 5/9 | ENST00000375353.5 | |
TMEM255B | NM_001348663.2 | c.405C>T | p.Tyr135= | synonymous_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM255B | ENST00000375353.5 | c.405C>T | p.Tyr135= | synonymous_variant | 5/9 | 1 | NM_182614.4 | P1 | |
TMEM255B | ENST00000488362.5 | c.405C>T | p.Tyr135= | synonymous_variant | 5/5 | 2 | |||
TMEM255B | ENST00000375348.3 | n.429C>T | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152222Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000728 AC: 183AN: 251382Hom.: 1 AF XY: 0.000751 AC XY: 102AN XY: 135892
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GnomAD4 exome AF: 0.00108 AC: 1579AN: 1461822Hom.: 1 Cov.: 31 AF XY: 0.00106 AC XY: 773AN XY: 727206
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GnomAD4 genome AF: 0.000630 AC: 96AN: 152340Hom.: 1 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | TMEM255B: BP4, BP7 - |
Computational scores
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BayesDel_noAF
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at