chr5-42800982-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005410.4(SELENOP):āc.884T>Cā(p.Leu295Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,614,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_005410.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENOP | NM_005410.4 | c.884T>C | p.Leu295Ser | missense_variant | 5/5 | ENST00000514985.6 | |
CCDC152 | NM_001134848.2 | c.*1201A>G | 3_prime_UTR_variant | 9/9 | ENST00000361970.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENOP | ENST00000514985.6 | c.884T>C | p.Leu295Ser | missense_variant | 5/5 | 1 | NM_005410.4 | P1 | |
CCDC152 | ENST00000361970.10 | c.*1201A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_001134848.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000595 AC: 147AN: 247064Hom.: 0 AF XY: 0.000499 AC XY: 67AN XY: 134258
GnomAD4 exome AF: 0.000280 AC: 409AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.000261 AC XY: 190AN XY: 727240
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74528
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at