rs767323746
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018133.4(MSL2):c.1332G>A(p.Met444Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018133.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSL2 | NM_018133.4 | c.1332G>A | p.Met444Ile | missense_variant | Exon 2 of 2 | ENST00000309993.3 | NP_060603.2 | |
MSL2 | NM_001145417.2 | c.1110G>A | p.Met370Ile | missense_variant | Exon 2 of 2 | NP_001138889.1 | ||
MSL2 | XM_005247571.4 | c.1110G>A | p.Met370Ile | missense_variant | Exon 2 of 2 | XP_005247628.1 | ||
MSL2 | XM_011512949.3 | c.1110G>A | p.Met370Ile | missense_variant | Exon 2 of 2 | XP_011511251.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251430Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135888
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461866Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1332G>A (p.M444I) alteration is located in exon 2 (coding exon 2) of the MSL2 gene. This alteration results from a G to A substitution at nucleotide position 1332, causing the methionine (M) at amino acid position 444 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at