chrX-50598480-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020717.5(SHROOM4):c.3998G>A(p.Arg1333Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,205,707 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.3998G>A | p.Arg1333Gln | missense_variant | 8/9 | ENST00000376020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.3998G>A | p.Arg1333Gln | missense_variant | 8/9 | 2 | NM_020717.5 | P1 | |
SHROOM4 | ENST00000289292.11 | c.3998G>A | p.Arg1333Gln | missense_variant | 8/10 | 1 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.3650G>A | p.Arg1217Gln | missense_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000624 AC: 7AN: 112114Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34262
GnomAD3 exomes AF: 0.0000292 AC: 5AN: 171114Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 56890
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1093593Hom.: 0 Cov.: 31 AF XY: 0.00000556 AC XY: 2AN XY: 359439
GnomAD4 genome ? AF: 0.0000624 AC: 7AN: 112114Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34262
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2013 | There is insufficient or conflicting evidence for classification of this alteration. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at