5-132823360-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001172700.2(SHROOM1):c.2116A>T(p.Met706Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000392 in 1,607,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHROOM1 | NM_001172700.2 | c.2116A>T | p.Met706Leu | missense_variant | 9/10 | ENST00000378679.8 | NP_001166171.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM1 | ENST00000378679.8 | c.2116A>T | p.Met706Leu | missense_variant | 9/10 | 1 | NM_001172700.2 | ENSP00000367950 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152270Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000171 AC: 4AN: 233360Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128894
GnomAD4 exome AF: 0.0000392 AC: 57AN: 1455578Hom.: 0 Cov.: 31 AF XY: 0.0000400 AC XY: 29AN XY: 724364
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.2116A>T (p.M706L) alteration is located in exon 9 (coding exon 6) of the SHROOM1 gene. This alteration results from a A to T substitution at nucleotide position 2116, causing the methionine (M) at amino acid position 706 to be replaced by a leucine (L). 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