chrX-50596772-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_020717.5(SHROOM4):c.4405G>A(p.Glu1469Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000107 in 1,210,509 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4405G>A | p.Glu1469Lys | missense_variant | Exon 9 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4405G>A | p.Glu1469Lys | missense_variant | Exon 9 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.4057G>A | p.Glu1353Lys | missense_variant | Exon 8 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.00000888 AC: 1AN: 112556Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34708
GnomAD3 exomes AF: 0.00000547 AC: 1AN: 182950Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67428
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097953Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 363323
GnomAD4 genome AF: 0.00000888 AC: 1AN: 112556Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34708
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4405G>A (p.E1469K) alteration is located in exon 9 (coding exon 9) of the SHROOM4 gene. This alteration results from a G to A substitution at nucleotide position 4405, causing the glutamic acid (E) at amino acid position 1469 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