chr7-135240636-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001394401.1(STRA8):c.112C>T(p.Arg38Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
STRA8
NM_001394401.1 missense
NM_001394401.1 missense
Scores
5
7
7
Clinical Significance
Conservation
PhyloP100: 1.99
Genes affected
STRA8 (HGNC:30653): (stimulated by retinoic acid 8) This gene encodes a retinoic acid-responsive protein. A homologous protein in mouse has been shown to be involved in the regulation of meiotic initiation in both spermatogenesis and oogenesis, though feature differences between the mouse and human proteins suggest that these homologs are not entirely functionally equivalent. It is thought that this gene may play a role in spermatogenesis in humans. [provided by RefSeq, Nov 2010]
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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=0.42030835).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRA8 | NM_001394401.1 | c.112C>T | p.Arg38Cys | missense_variant | 2/9 | ENST00000662584.2 | |
STRA8 | NM_182489.3 | c.112C>T | p.Arg38Cys | missense_variant | 2/9 | ||
STRA8 | XM_011516137.3 | c.112C>T | p.Arg38Cys | missense_variant | 1/8 | ||
STRA8 | XM_047420324.1 | c.112C>T | p.Arg38Cys | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRA8 | ENST00000662584.2 | c.112C>T | p.Arg38Cys | missense_variant | 2/9 | NM_001394401.1 | P2 | ||
STRA8 | ENST00000275764.3 | c.178C>T | p.Arg60Cys | missense_variant | 2/9 | 1 | A2 | ||
STRA8 | ENST00000667288.1 | c.112C>T | p.Arg38Cys | missense_variant | 2/9 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152152Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251208Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135870
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GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461862Hom.: 0 Cov.: 35 AF XY: 0.0000234 AC XY: 17AN XY: 727228
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74452
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.178C>T (p.R60C) alteration is located in exon 2 (coding exon 2) of the STRA8 gene. This alteration results from a C to T substitution at nucleotide position 178, causing the arginine (R) at amino acid position 60 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Uncertain
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Pathogenic
D
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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