chr4-76739349-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_020859.4(SHROOM3):c.1176C>T(p.Tyr392Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
SHROOM3
NM_020859.4 synonymous
NM_020859.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.664
Genes affected
SHROOM3 (HGNC:30422): (shroom family member 3) This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP7
Synonymous conserved (PhyloP=-0.664 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SHROOM3 | NM_020859.4 | c.1176C>T | p.Tyr392Tyr | synonymous_variant | 5/11 | ENST00000296043.7 | NP_065910.3 | |
| SHROOM3-AS1 | NR_187404.1 | n.1044+3459G>A | intron_variant | |||||
| SHROOM3-AS1 | NR_187405.1 | n.500+3459G>A | intron_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SHROOM3 | ENST00000296043.7 | c.1176C>T | p.Tyr392Tyr | synonymous_variant | 5/11 | 1 | NM_020859.4 | ENSP00000296043.6 |
Frequencies
GnomAD3 genomes 0.0000328 AC: 5AN: 152234Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250444Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135510
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461752Hom.: 0 Cov.: 78 AF XY: 0.0000138 AC XY: 10AN XY: 727158
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GnomAD4 genome 0.0000328 AC: 5AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74372
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at