rs33003
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002439.5(MSH3):c.3303-436A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 149,824 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 0.000013 ( 0 hom., cov: 29)
Consequence
MSH3
NM_002439.5 intron
NM_002439.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.223
Genes affected
MSH3 (HGNC:7326): (mutS homolog 3) The protein encoded by this gene forms a heterodimer with MSH2 to form MutS beta, part of the post-replicative DNA mismatch repair system. MutS beta initiates mismatch repair by binding to a mismatch and then forming a complex with MutL alpha heterodimer. This gene contains a polymorphic 9 bp tandem repeat sequence in the first exon. The repeat is present 6 times in the reference genome sequence and 3-7 repeats have been reported. Defects in this gene are a cause of susceptibility to endometrial cancer. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH3 | ENST00000265081.7 | c.3303-436A>C | intron_variant | Intron 23 of 23 | 1 | NM_002439.5 | ENSP00000265081.6 | |||
MSH3 | ENST00000658259.1 | c.3135-436A>C | intron_variant | Intron 23 of 23 | ENSP00000499617.1 | |||||
MSH3 | ENST00000667069.1 | c.3108-436A>C | intron_variant | Intron 21 of 21 | ENSP00000499502.1 | |||||
MSH3 | ENST00000670357.1 | n.*627-436A>C | intron_variant | Intron 24 of 24 | ENSP00000499791.1 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 149824Hom.: 0 Cov.: 29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000133 AC: 2AN: 149824Hom.: 0 Cov.: 29 AF XY: 0.0000274 AC XY: 2AN XY: 73078
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at