rs28937871
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040108.2(MLH3):āc.1496A>Gā(p.Asn499Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001040108.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLH3 | NM_001040108.2 | c.1496A>G | p.Asn499Ser | missense_variant | 2/13 | ENST00000355774.7 | NP_001035197.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLH3 | ENST00000355774.7 | c.1496A>G | p.Asn499Ser | missense_variant | 2/13 | 5 | NM_001040108.2 | ENSP00000348020.2 | ||
MLH3 | ENST00000380968.6 | c.1496A>G | p.Asn499Ser | missense_variant | 2/12 | 1 | ENSP00000370355.3 | |||
MLH3 | ENST00000556257.5 | c.1496A>G | p.Asn499Ser | missense_variant | 2/7 | 5 | ENSP00000451540.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251212Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135794
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461770Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727174
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Colorectal cancer, hereditary nonpolyposis, type 7 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Apr 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at