chrX-50598413-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_020717.5(SHROOM4):c.4065C>T(p.Ala1355=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,207,709 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A1355A) has been classified as Likely benign.
Frequency
Consequence
NM_020717.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.4065C>T | p.Ala1355= | synonymous_variant | 8/9 | ENST00000376020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4065C>T | p.Ala1355= | synonymous_variant | 8/9 | 2 | NM_020717.5 | P1 | |
SHROOM4 | ENST00000289292.11 | c.4065C>T | p.Ala1355= | synonymous_variant | 8/10 | 1 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.3717C>T | p.Ala1239= | synonymous_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000897 AC: 1AN: 111540Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33722
GnomAD3 exomes AF: 0.00000565 AC: 1AN: 177128Hom.: 0 AF XY: 0.0000161 AC XY: 1AN XY: 62022
GnomAD4 exome AF: 0.00000730 AC: 8AN: 1096169Hom.: 0 Cov.: 32 AF XY: 0.00000830 AC XY: 3AN XY: 361653
GnomAD4 genome ? AF: 0.00000897 AC: 1AN: 111540Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33722
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | SHROOM4: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at