chr5-80654922-G-GCCCCCAGCT
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_002439.5(MSH3):c.199_207dupCCAGCTCCC(p.Pro67_Pro69dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 20)
Exomes 𝑓: 0.000017 ( 1 hom. )
Consequence
MSH3
NM_002439.5 conservative_inframe_insertion
NM_002439.5 conservative_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0550
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]
DHFR (HGNC:2861): (dihydrofolate reductase) Dihydrofolate reductase converts dihydrofolate into tetrahydrofolate, a methyl group shuttle required for the de novo synthesis of purines, thymidylic acid, and certain amino acids. While the functional dihydrofolate reductase gene has been mapped to chromosome 5, multiple intronless processed pseudogenes or dihydrofolate reductase-like genes have been identified on separate chromosomes. Dihydrofolate reductase deficiency has been linked to megaloblastic anemia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_002439.5.
BS2
High AC in GnomAdExome4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSH3 | NM_002439.5 | c.199_207dupCCAGCTCCC | p.Pro67_Pro69dup | conservative_inframe_insertion | Exon 1 of 24 | ENST00000265081.7 | NP_002430.3 | |
DHFR | NM_000791.4 | c.-442_-434dupAGCTGGGGG | 5_prime_UTR_variant | Exon 1 of 6 | ENST00000439211.7 | NP_000782.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH3 | ENST00000265081.7 | c.199_207dupCCAGCTCCC | p.Pro67_Pro69dup | conservative_inframe_insertion | Exon 1 of 24 | 1 | NM_002439.5 | ENSP00000265081.6 | ||
MSH3 | ENST00000667069.1 | c.199_207dupCCAGCTCCC | p.Pro67_Pro69dup | conservative_inframe_insertion | Exon 1 of 22 | ENSP00000499502.1 | ||||
DHFR | ENST00000439211.7 | c.-442_-434dupAGCTGGGGG | 5_prime_UTR_variant | Exon 1 of 6 | 1 | NM_000791.4 | ENSP00000396308.2 | |||
MSH3 | ENST00000670357.1 | n.199_207dupCCAGCTCCC | non_coding_transcript_exon_variant | Exon 1 of 25 | ENSP00000499791.1 |
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD3 genomes
Cov.:
20
GnomAD3 exomes AF: 0.0000237 AC: 3AN: 126454Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 71060
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GnomAD4 exome AF: 0.0000167 AC: 23AN: 1380954Hom.: 1 Cov.: 16 AF XY: 0.0000132 AC XY: 9AN XY: 683602
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GnomAD4 genome Cov.: 20
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20
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Endometrial carcinoma;C4310719:Familial adenomatous polyposis 4 Uncertain:1
Feb 29, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at