rs77542170

chr1-45332088-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 12P and 5B. PVS1 PP3_Strong BS1_Supporting BS2

The NM_001048174.2(MUTYH):c.850-2A>G variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000561 in 1,614,184 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00054 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00056 (13 hom.)
• Consequence: MUTYH NM_001048174.2 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:7 B:7 O:1
• Conservation: PhyloP100: 3.12

Genes affected

MUTYH (HGNC:7527): (mutY DNA glycosylase) This gene encodes a DNA glycosylase involved in oxidative DNA damage repair. The enzyme excises adenine bases from the DNA backbone at sites where adenine is inappropriately paired with guanine, cytosine, or 8-oxo-7,8-dihydroguanine, a major oxidatively damaged DNA lesion. The protein is localized to the nucleus and mitochondria. This gene product is thought to play a role in signaling apoptosis by the introduction of single-strand breaks following oxidative damage. Mutations in this gene result in heritable predisposition to colorectal cancer, termed MUTYH-associated polyposis (MAP). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PVS1: Splicing variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• BS1: Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000563 (823/1461890) while in subpopulation EAS AF= 0.019 (755/39700). AF 95% confidence interval is 0.0179. There are 13 homozygotes in gnomad4_exome. There are 397 alleles in male gnomad4_exome subpopulation. Median coverage is 36. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAdExome at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUTYH	NM_001048174.2	c.850-2A>G		splice_acceptor_variant		ENST00000456914.7
MUTYH	NM_001128425.2	c.934-2A>G		splice_acceptor_variant		ENST00000710952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUTYH	ENST00000456914.7	c.850-2A>G		splice_acceptor_variant		1	NM_001048174.2	A1
MUTYH	ENST00000710952.2	c.934-2A>G		splice_acceptor_variant			NM_001128425.2

Frequencies

GnomAD3 genomes AF: 0.000532 AC: 81 AN: 152176 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00113 AC: 285 AN: 251466 Hom.: 5 AF XY: 0.00113 AC XY: 153 AN XY: 135916

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0152

Gnomad SAS exome AF: 0.000131

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000563 AC: 823 AN: 1461890 Hom.: 13 Cov.: 36 AF XY: 0.000546 AC XY: 397 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0190

Gnomad4 SAS exome AF: 0.000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000360

Gnomad4 OTH exome AF: 0.000729

GnomAD4 genome AF: 0.000545 AC: 83 AN: 152294 Hom.: 1 Cov.: 33 AF XY: 0.000685 AC XY: 51 AN XY: 74464

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000675 Hom.: 1

Bravo AF: 0.000453

ExAC AF: 0.00102 AC: 124

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:7 Benign:7 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Familial adenomatous polyposis 2 Pathogenic:3 Uncertain:2 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 04, 2020	This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Likely pathogenic, no assertion criteria provided	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jul 13, 2012	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Pathogenic, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Division of Medical Genetics, University of Washington	Jan 03, 2019	The c.934-2A>G variant is predicted to lead to either nonsense-mediated mRNA decay or an abnormal protein product by destroying a canonical splice acceptor site. In vitro studies of this variant have demonstrated aberrant splicing and that the variant protein, if translated, is not localized to the nucleus (Tao 2004, Taki 2016). The c.934-2A>G variant was identified in 1.6% of East Asian chromosomes in the Genome Aggregation Database (http://gnomad.broadinstitute.org). This variant has been reported in the literature in a heterozygous state in multiple individuals with colorectal cancer; however has never, to our knowledge, been reported in an affected individual that is homozygous or compound heterozygous for a second MUTYH pathogenic variant (Miyaki 2005, Kim 2007, Taki 2016). -

not provided Uncertain:3 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 18, 2023	This variant occurs at a canonical splice-acceptor site and is predicted to interfere with normal MUTYH mRNA splicing. Functional studies report that this variant results in aberrant transcripts (PMIDs: 15180946 (2004), 26684191 (2016) 30833417 (2019)), however, a recent RNA study demonstrates this variant exclusively results in the in-frame deletion of three amino acids and is unlikely to cause a significant effect on protein function (PMID: 34716202 (2022)). The frequency of this variant in the general population, 0.015 (223/14422 chromosomes in Other East Asian subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals with colorectal polyps (PMID: 28251689 (2017), 29330641 (2018), 34716202 (2022)), colorectal cancer (PMID: 33563768 (2022), 34716202 (2022), 35098669 (2022)), breast cancer (PMID: 34716202 (2022), 35264596 (2022), 36119527 (2022)), familial adenomatous polyposis (FAP) (PMID: 17703316 (2007), 26837502 (2016)), as well as other cancer types. This variant is also reported in unaffected individuals (PMID: 28332257 (2017), 33309985 (2020), 33471991 (2021), https://databases.lovd.nl/shared/variants/MUTYH). Based on the available information, we are unable to determine the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 04, 2021	The MUTYH c.934-2A>G variant (rs77542170), also known as IVS10-2A>G or c.892-2A>G for NM_001048171, is reported in the literature in multiple individuals with colorectal adenomatous polyposis or colorectal cancer, but has only been reported in the heterozygous state with no additional MUTYH variant identified (Hansen 2017, Taki 2016, Zhang 2017). This variant has also been reported heterozygously in individuals with breast and/or ovarian cancer (Hirotsu 2015, Kurian 2014) as well as an individual with glioma (Kline 2016). This variant is found heterozygously at a similar frequency in individuals with gastric cancer as in controls (Tao 2004). This variant disrupts the canonical splice acceptor site of intron 10, and RNA analysis shows this alters splicing and causes intron 10 retention leading to a premature termination codon; however the proportion of aberrant transcripts compared to wild type is unclear (Tao 2004). This variant is also reported in the ClinVar database (Variation ID: 41766) and is found in the East Asian population with an allele frequency of 1.5% (307/19952 alleles, including 5 homozygotes) in the Genome Aggregation Database, which is greater than expected for a pathogenic variant. Due to conflicting information, the clinical significance of the c.934-2A>G variant is uncertain at this time. -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 01, 2023	See Variant Classification Assertion Criteria. -

not specified Uncertain:1 Benign:2 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jul 01, 2020	The c.934-2A>G variant in MUTYH has been widely studied in the East Asian population and reported in at least 7 individuals with colorectal cancer; however, to our knowledge, none of these individuals had a second pathogenic germline MUTYH variant identified (Miyaki 2005 PMID:15890374, Kim 2007 PMID:17703316, Taki 2016 PMID:26684191). It has been identified in 1.54% (307/19952) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 41766). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Functional studies was demonstrated to cause aberrant splicing in in vitro studies (Tao 2004 PMID:15180946, Taki 2016 PMID:26684191), but whether this alteration causes a biological loss of function of the MUTYH protein in humans is uncertain. In summary, while the predicted functional impact of this variant and in vitro studies favor a pathogenic role, based on the absence of reported affected individuals carrying this variant and a second pathogenic MUTYH variant in the literature despite its high frequency in the general population, its clinical significance is uncertain. Additional studies are needed to clarify the significance of this variant. ACMG/AMP Criteria applied: BS1_Supporting. -
not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 28, 2023	Variant summary: MUTYH c.934-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes the canonical 3' splicing acceptor site, while two predict the variant creates a novel 3' acceptor site, 9 nucleotides downstream from the original splice site. Earlier RNA studies reported that this variant affects mRNA splicing, resulting in the out-of-frame inclusion of intron 10, causing a premature translation stop signal (Tao_2004, Taki_2016, Thibodeau_2019), in addition, an abnormal splicing event removing 9 bp from the 5' end of exon 11 was also described (Taki_2016, Thibodeau_2019). However, a recent detailed analysis (Hernandez_2022) demonstrated that the out-of-frame inclusion of intron 10 is a naturally occurring, low-level alternative splicing event (detected in both variant carrier and control samples, in about 5-13% of transcripts), while the variant exclusively results in the in-frame deletion of 9 nucleotides from the 5' end of exon 11 (detected in about 22-29% of the transcripts). This deletion causes an in-frame loss of three amino acids (p.V312_Q314del), which is not located to any known domains (InterPro), but is predicted to be positioned within a flexible linker region between domains, which does not engage in any apparent specific interactions (Hernandez_2022). The variant allele was found at a frequency of 0.0012 in 253188 control chromosomes (gnomAD and publication data), predominantly at a frequency of 0.015 within the East Asian subpopulation (in the gnomAD database), including 5 homozygotes. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 3-fold of the estimated maximal expected allele frequency for a pathogenic variant in MUTYH causing MUTYH-Associated Polyposis (MAP) phenotype (0.0046). In addition, this variant was found at an even higher allele frequency in two Japanese control databases, jMorp and HGVD-Kyoto, with allele frequencies of 0.0195 and 0.0248, respectively. These data suggest that this variant is a benign polymorphism found primarily in populations of East Asian origin. c.934-2A>G has been reported in the literature in multiple individuals affected with colorectal polyposis, and other tumor phenotypes, including e.g. breast-, ovarian-, gallbladder-, colon-, endometrial- and thyroid cancer (e.g. Miyaki_2005, Kim_2007, Frey_2015, Hirotsu_2015, Taki_2016, Hansen_2017, Li_2017, Zhang_2017, Chan_2018, Thibodeau_2019, Wang_2019, Slavin_2020). However, none of the reported individuals with colorectal polyposis were indicated to be compound heterozygotes or homozygotes for MUTYH mutations. A recent case-control study in the Japanese population identified the variant in heterozygous state at a high frequency in both controls and colorectal cancer (CRC) cases, and found it in homozygous CRC patients (4 cases) who did not have multiple polyps, indicating that the variant is likely to be non-causative (Fujita_2020). A recent study also noted the lack of a polyposis phenotype in three biallelic carriers (Hernandez_2022). We also ascertained two studies reporting homozygous occurrences of the variant in a patient diagnosed with gastric cancer, and in a patient with endometrial cancer, without strong evidence of causality (Tao_2004, Wang_2019). A publication (Jian_2017) reported two independent breast cancer patients who did not carry the variant of interest, while some of their unaffected daughters (younger than the average age of onset for breast cancer) carried the variant. In addition, in a recent large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 253/60466 cases (allele frequency of 0.001) and 236/53461 contro -
Likely benign, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -

Hereditary cancer-predisposing syndrome Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 14, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 29, 2019	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Carcinoma of colon Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MUTYH c.934-2A>G variant was identified in 19 of 2400 proband chromosomes and 1 homozygous proband at a frequency of 0.025 from East Asian (Japanese, Chinese and Korean) individuals with colorectal polyps and/or colorectal, gastric and breast cancers and was present in 21 of 1206 control chromosomes (frequency: 0.014) from healthy individuals (Tao 2004, Lin 2016, Zhang 2017, Miyaki 2005, Jang 2015, Johnston 2012, Taki 2016 and Kim 2007). The variant was also identified in the following databases: dbSNP (ID: rs77542170 as “With other allele”) and ClinVar (1x as pathogenic by Soonchunhyang University Bucheon Hospital; 4x as likely pathogenic by Invitae, GeneDx, Quest Diagnostics, and Biesecker Lab/NIH; and 3x as uncertain significance by Ambry Genetics, Laboratory for Molecular Medicine, and Integrated Genetics/Laboratory Corporation of America). The variant was not identified in the Cosmic, MutDB or UMD-LSDB databases. The variant was identified in control databases in 298 of 277146 chromosomes (5 homozygous) at a frequency of 0.001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 293 of 18870 chromosomes (5 homozygous, freq: 0.015), and South Asian in 5 of 30782 chromosomes (freq: 0.0002) and the variant was not observed in the African, Other, Latino, European Non-Finnish, Ashkenazi Jewish or Finnish populations. The c.934-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence, and 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. Two independent studies have shown the MUTYH c.934-2A>G variant results in an aberrant mRNA transcript which retains intron 10, has a premature stop codon in exon 11, and encodes a truncated protein (Tao 2004 and Taki 2015). Further, in vitro expression studies demonstrate that, if translated, the variant protein is not localized in the nucleus like the wild type protein, suggesting insufficient ability of the variant protein to repair nuclear DNA (Tao 2004). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -

Gastric cancer Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Nov 03, 2018

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has previously been reported as disease-causing [PMID 15180946, 22703879, 24733792, 24728327] With updated public general population genomic data and literatures, we now reclassified this variant as likely pathogenic [PMID 26332594, 26684149] -

MUTYH-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 01, 2024

The MUTYH c.934-2A>G variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant, also referred to as IVS10-2A>G or c.892-2A>G, was observed in East Asian individuals with gastric cancer (Tao et al. 2004. PubMed ID: 15180946), with breast/ovarian cancers (Hirotsu et al. 2015. PubMed ID: 26436112; Kurian et al. 2014. PubMed ID: 24733792; Lin et al. 2016. PubMed ID: 26824983), with colorectal polyposis/multiple colorectal adenomas (Taki et al. 2016. PubMed ID: 26684191; Tian et al. 2020. PubMed ID: 32904697), and in a patient with pancreatic ductal adenocarcinoma (Cremin et al. 2020. PubMed ID: 32255556). No significant difference in the distribution of the MUTYH c.934-2A>G variant was found between the gastric cancer cases and controls and, to date, only one individual with gastric cancer was reported to be homozygous for this variant (Tao et al. 2004. PubMed ID: 15180946). In fact, this variant is reported in 1.5% of alleles in individuals of East Asian descent in gnomAD, including 5 homozygotes (http://gnomad.broadinstitute.org), which are assumed to be cancer free. Therefore, this frequency is higher than expected for a pathogenic variant in this gene. Initial RNA studies of cancer patients' blood have suggested that this variant in intron 11 results in an aberrant mRNA transcript retaining intron 10, resulting in frameshift and premature termination. However, this transcript was also present in healthy wild-type individuals, although at a lower level, suggesting that it represents a natural alternative splicing (Tao et al. 2004. PubMed ID: 15180946; Taki et al. 2016. PubMed ID: 26684191; Hernandez et al. 2022. PubMed ID: 34716202). A later study detected the presence of another transcript, this time exhibiting an in-frame deletion of 9 nucleotides at the 5' end of exon 11, and only in the blood of affected individuals (Hernandez et al. 2022. PubMed ID: 34716202). This aberrant splicing results in the loss of 3 amino acids (p.Val312_Glu314del), which is unlikely to have a significant effect on protein function. In addition, this variant has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from likely benign to pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/41766/). Although we suspect that this variant may be benign, the clinical significance of this variant is classified as uncertain at this time due to insufficient functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Uncertain	-0.040
Cadd	Pathogenic	27
Dann	Benign	0.96
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D
GERP RS		5.3

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.78
SpliceAI score (max)		0.95		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.32		Position offset: -11
DS_AL_spliceai		0.95		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs77542170; hg19: chr1-45797760;