rs1311902654

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001395507.1(TMPRSS7):​c.832G>A​(p.Val278Met) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

TMPRSS7
NM_001395507.1 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.33
Variant links:
Genes affected
TMPRSS7 (HGNC:30846): (transmembrane serine protease 7) Predicted to enable serine-type peptidase activity. Predicted to be involved in proteolysis. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2960742).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMPRSS7NM_001395507.1 linkc.832G>A p.Val278Met missense_variant Exon 7 of 18 ENST00000452346.7 NP_001382436.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMPRSS7ENST00000452346.7 linkc.832G>A p.Val278Met missense_variant Exon 7 of 18 5 NM_001395507.1 ENSP00000398236.2 Q7RTY8-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.014
T;.;.;.
Eigen
Uncertain
0.25
Eigen_PC
Uncertain
0.31
FATHMM_MKL
Benign
0.62
D
LIST_S2
Uncertain
0.91
D;.;D;D
M_CAP
Benign
0.0068
T
MetaRNN
Benign
0.30
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.90
L;.;.;.
PrimateAI
Benign
0.37
T
PROVEAN
Benign
0.90
N;N;.;N
REVEL
Benign
0.11
Sift
Benign
0.086
T;T;.;D
Sift4G
Benign
0.10
T;T;T;D
Polyphen
0.88
P;P;P;.
Vest4
0.23
MutPred
0.51
Gain of MoRF binding (P = 0.1346);.;.;.;
MVP
0.57
MPC
0.30
ClinPred
0.85
D
GERP RS
3.1
Varity_R
0.035
gMVP
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1311902654; hg19: chr3-111766687; API