rs145292294
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020717.5(SHROOM4):āc.4079A>Gā(p.Asn1360Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000389 in 1,208,421 control chromosomes in the GnomAD database, including 2 homozygotes. There are 13 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4079A>G | p.Asn1360Ser | missense_variant | Exon 8 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4079A>G | p.Asn1360Ser | missense_variant | Exon 8 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.3731A>G | p.Asn1244Ser | missense_variant | Exon 7 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.0000718 AC: 8AN: 111399Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33589
GnomAD3 exomes AF: 0.0000669 AC: 12AN: 179414Hom.: 1 AF XY: 0.0000468 AC XY: 3AN XY: 64092
GnomAD4 exome AF: 0.0000356 AC: 39AN: 1097022Hom.: 2 Cov.: 32 AF XY: 0.0000304 AC XY: 11AN XY: 362430
GnomAD4 genome AF: 0.0000718 AC: 8AN: 111399Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33589
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4079A>G (p.N1360S) alteration is located in exon 8 (coding exon 8) of the SHROOM4 gene. This alteration results from a A to G substitution at nucleotide position 4079, causing the asparagine (N) at amino acid position 1360 to be replaced by a serine (S). 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