chr5-132824705-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001172700.2(SHROOM1):c.1151C>A(p.Ser384Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,126 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM1 | NM_001172700.2 | c.1151C>A | p.Ser384Tyr | missense_variant | 6/10 | ENST00000378679.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM1 | ENST00000378679.8 | c.1151C>A | p.Ser384Tyr | missense_variant | 6/10 | 1 | NM_001172700.2 | P2 | |
SHROOM1 | ENST00000319854.7 | c.1151C>A | p.Ser384Tyr | missense_variant | 3/7 | 1 | A2 | ||
SHROOM1 | ENST00000617339.4 | c.1151C>A | p.Ser384Tyr | missense_variant | 4/8 | 5 | P2 | ||
SHROOM1 | ENST00000378676.1 | c.1035-286C>A | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251436Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135910
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461812Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727212
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.1151C>A (p.S384Y) alteration is located in exon 6 (coding exon 3) of the SHROOM1 gene. This alteration results from a C to A substitution at nucleotide position 1151, causing the serine (S) at amino acid position 384 to be replaced by a tyrosine (Y). 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