chr5-132824298-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001172700.2(SHROOM1):c.1363C>A(p.Gln455Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000574 in 1,613,662 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001172700.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM1 | NM_001172700.2 | c.1363C>A | p.Gln455Lys | missense_variant | 7/10 | ENST00000378679.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM1 | ENST00000378679.8 | c.1363C>A | p.Gln455Lys | missense_variant | 7/10 | 1 | NM_001172700.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152228Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000473 AC: 118AN: 249310Hom.: 1 AF XY: 0.000482 AC XY: 65AN XY: 134776
GnomAD4 exome AF: 0.000584 AC: 853AN: 1461316Hom.: 2 Cov.: 33 AF XY: 0.000572 AC XY: 416AN XY: 726920
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152346Hom.: 1 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1363C>A (p.Q455K) alteration is located in exon 7 (coding exon 4) of the SHROOM1 gene. This alteration results from a C to A substitution at nucleotide position 1363, causing the glutamine (Q) at amino acid position 455 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