chr11-113690335-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_030770.4(TMPRSS5):āc.1102T>Cā(p.Leu368=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 1,601,632 control chromosomes in the GnomAD database, including 359,486 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.74 ( 42358 hom., cov: 29)
Exomes š: 0.66 ( 317128 hom. )
Consequence
TMPRSS5
NM_030770.4 synonymous
NM_030770.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0150
Genes affected
TMPRSS5 (HGNC:14908): (transmembrane serine protease 5) This gene encodes a protein that belongs to the serine protease family. Serine proteases are known to be involved in many physiological and pathological processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 11-113690335-A-G is Benign according to our data. Variant chr11-113690335-A-G is described in ClinVar as [Benign]. Clinvar id is 508108.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.015 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMPRSS5 | NM_030770.4 | c.1102T>C | p.Leu368= | synonymous_variant | 11/13 | ENST00000299882.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMPRSS5 | ENST00000299882.11 | c.1102T>C | p.Leu368= | synonymous_variant | 11/13 | 1 | NM_030770.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.738 AC: 111652AN: 151200Hom.: 42298 Cov.: 29
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GnomAD3 exomes AF: 0.688 AC: 159386AN: 231606Hom.: 55241 AF XY: 0.680 AC XY: 84907AN XY: 124954
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GnomAD4 exome AF: 0.658 AC: 955023AN: 1450312Hom.: 317128 Cov.: 60 AF XY: 0.658 AC XY: 473561AN XY: 719962
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GnomAD4 genome AF: 0.739 AC: 111772AN: 151320Hom.: 42358 Cov.: 29 AF XY: 0.737 AC XY: 54463AN XY: 73850
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at