X-50635342-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_020717.5(SHROOM4):āc.731A>Gā(p.Asn244Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 1,200,910 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 103 hemizygotes in GnomAD. 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 Likely benign (ā ā ).
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.731A>G | p.Asn244Ser | missense_variant | 4/9 | ENST00000376020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.731A>G | p.Asn244Ser | missense_variant | 4/9 | 2 | NM_020717.5 | P1 | |
SHROOM4 | ENST00000289292.11 | c.731A>G | p.Asn244Ser | missense_variant | 4/10 | 1 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.383A>G | p.Asn128Ser | missense_variant | 3/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000259 AC: 29AN: 111810Hom.: 0 Cov.: 23 AF XY: 0.000235 AC XY: 8AN XY: 34006
GnomAD3 exomes AF: 0.000268 AC: 43AN: 160256Hom.: 0 AF XY: 0.000139 AC XY: 7AN XY: 50276
GnomAD4 exome AF: 0.000314 AC: 342AN: 1089051Hom.: 0 Cov.: 33 AF XY: 0.000267 AC XY: 95AN XY: 356303
GnomAD4 genome AF: 0.000259 AC: 29AN: 111859Hom.: 0 Cov.: 23 AF XY: 0.000235 AC XY: 8AN XY: 34065
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 26, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at