X-50596946-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020717.5(SHROOM4):āc.4231A>Cā(p.Lys1411Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000703 in 1,209,183 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4231A>C | p.Lys1411Gln | missense_variant | Exon 9 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4231A>C | p.Lys1411Gln | missense_variant | Exon 9 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.3883A>C | p.Lys1295Gln | missense_variant | Exon 8 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.0000356 AC: 4AN: 112512Hom.: 0 Cov.: 24 AF XY: 0.0000577 AC XY: 2AN XY: 34664
GnomAD3 exomes AF: 0.000371 AC: 66AN: 178054Hom.: 0 AF XY: 0.000269 AC XY: 17AN XY: 63214
GnomAD4 exome AF: 0.0000739 AC: 81AN: 1096618Hom.: 0 Cov.: 31 AF XY: 0.0000580 AC XY: 21AN XY: 362098
GnomAD4 genome AF: 0.0000355 AC: 4AN: 112565Hom.: 0 Cov.: 24 AF XY: 0.0000576 AC XY: 2AN XY: 34727
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4231A>C (p.K1411Q) alteration is located in exon 9 (coding exon 9) of the SHROOM4 gene. This alteration results from a A to C substitution at nucleotide position 4231, causing the lysine (K) at amino acid position 1411 to be replaced by a glutamine (Q). 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