3-37014548-A-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000249.4(MLH1):c.790+4A>G variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MLH1 NM_000249.4 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9944
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 2.93

Genes affected

MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 3-37014548-A-G is Pathogenic according to our data. Variant chr3-37014548-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-37014548-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.790+4A>G		splice_donor_region_variant, intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.790+4A>G		splice_donor_region_variant, intron_variant		1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 22

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Oct 24, 2023	Criteria applied: PS3_MOD,PS4_MOD,PM2_SUP,PP3 -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 18, 2023	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data, PMID: 16341550]. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 27363726]. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 27, 2022	- -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The c.790+4A>G variant is located in the 5' splice region but does not affect the highly conserved +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions are known to sometimes affect splicing. The c.790+4A>G variant has been previously reported in the literature in 1 proband who had HNPCC and in another proband with colon cancer and his affected father (Mangold 2005; Wehner 1997). Pagenstecher 2006 studied the index patient from Mangold 2005 and by RT-PCR and agorose-gel electrophoresis demonstrated two shorter fragments suggesting a lack of either exon 9 or both exon 9 and 10, but definitive proof was lacking. Our laboratory has identified this variant in two individuals who were MLH1 deficient and segregation of the variant with disease was shown in 4 affected family members (one obligate carrier), increasing the likelihood this is a pathogenic variant. In addition, a different nucleotide change at the same position, c.790+4A>T, has been identified in one family with colon cancer including 5 informative meiosis and functional analysis demonstrating that this substitution leads to a complete skip of both exon 9 and 10 of the variant allele (Blanchi 2011). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

May 27, 2021

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the c.790+4 nucleotide in the MLH1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 20717847). This suggests that this nucleotide is clinically-significant, and that variants that disrupt this position are likely to be disease-causing. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with the skipping of exon 9, which introduces a frameshift (PMID: 16341550). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant has been observed in individual(s) with Lynch syndrome (PMID: 9298827, 16341550). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 90363). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 9 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 09, 2019

The c.790+4A>G intronic variant results from an A to G substitution 4 nucleotides after coding exon 9 in the MLH1 gene. This alteration was seen in a family meeting Amsterdam criteria whose proband was diagnosed with colorectal cancer at age 25. The proband's tumor exhibited microsatellite instability and absent MLH1 staining on IHC. In addition, RNA analyses from this patient and his positive affected father demonstrated partial exon skipping (Pagenstecher C et al. Hum. Genet., 2006 Mar;119:9-22). This alteration was previously identified in an additional family meeting Amsterdam criteria, but clinical details were not provided (Lamberti C et al. Gut, 1999 Jun;44:839-43). This nucleotide position is not well conserved in available vertebrate species. Using two different splice site prediction tools, this alteration is predicted by ESEfinder to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by BDGP; however, direct evidence is unavailable. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Uncertain	23
Dann	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.95
SpliceAI score (max)		0.83		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.83		Position offset: -4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs267607786; hg19: chr3-37056039;