11-106009857-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032424.3(MSANTD4):c.716G>A(p.Arg239Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,572 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R239S) has been classified as Uncertain significance.
Frequency
Consequence
NM_032424.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSANTD4 | ENST00000301919.9 | c.716G>A | p.Arg239Lys | missense_variant | Exon 3 of 3 | 1 | NM_032424.3 | ENSP00000304713.4 | ||
MSANTD4 | ENST00000530788.1 | c.*127G>A | downstream_gene_variant | 1 | ENSP00000435125.1 | |||||
MSANTD4 | ENST00000529805.1 | n.-109G>A | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461572Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727090
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.716G>A (p.R239K) alteration is located in exon 3 (coding exon 2) of the MSANTD4 gene. This alteration results from a G to A substitution at nucleotide position 716, causing the arginine (R) at amino acid position 239 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.