X-11758742-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001193270.2(MSL3):c.35C>T(p.Ala12Val) 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 1,165,592 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001193270.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSL3 | NM_078629.4 | c.102+377C>T | intron_variant | ENST00000312196.10 | NP_523353.2 | |||
MSL3 | NM_001193270.2 | c.35C>T | p.Ala12Val | missense_variant | 1/13 | NP_001180199.1 | ||
MSL3 | NM_078628.2 | c.102+377C>T | intron_variant | NP_523352.1 | ||||
MSL3 | NM_001282174.1 | c.-263+377C>T | intron_variant | NP_001269103.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000187 AC: 21AN: 112402Hom.: 0 Cov.: 23 AF XY: 0.000174 AC XY: 6AN XY: 34558
GnomAD3 exomes AF: 0.0000277 AC: 3AN: 108185Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 39395
GnomAD4 exome AF: 0.0000247 AC: 26AN: 1053136Hom.: 0 Cov.: 31 AF XY: 0.0000145 AC XY: 5AN XY: 344540
GnomAD4 genome AF: 0.000187 AC: 21AN: 112456Hom.: 0 Cov.: 23 AF XY: 0.000173 AC XY: 6AN XY: 34622
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2022 | 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