14-75014665-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001040108.2(MLH3):c.*2417G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 204,380 control chromosomes in the GnomAD database, including 17,304 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.40 (12934 hom., cov: 33)
  • Exomes 𝑓: 0.39 (4370 hom.)
• Consequence: MLH3 NM_001040108.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.50

Genes affected

MLH3 (HGNC:7128): (mutL homolog 3) This gene is a member of the MutL-homolog (MLH) family of DNA mismatch repair (MMR) genes. MLH genes are implicated in maintaining genomic integrity during DNA replication and after meiotic recombination. The protein encoded by this gene functions as a heterodimer with other family members. Somatic mutations in this gene frequently occur in tumors exhibiting microsatellite instability, and germline mutations have been linked to hereditary nonpolyposis colorectal cancer type 7 (HNPCC7). Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 14-75014665-C-T is Benign according to our data. Variant chr14-75014665-C-T is described in ClinVar as [Benign]. Clinvar id is 314351.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH3	NM_001040108.2	c.*2417G>A		3_prime_UTR_variant	13/13	ENST00000355774.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH3	ENST00000355774.7	c.*2417G>A		3_prime_UTR_variant	13/13	5	NM_001040108.2	P1
MLH3	ENST00000380968.6	c.*2417G>A		3_prime_UTR_variant	12/12	1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61416 AN: 151864 Hom.: 12927 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.393 AC: 20598 AN: 52398 Hom.: 4370 Cov.: 0 AF XY: 0.397 AC XY: 9663 AN XY: 24364

Gnomad4 AFR exome AF: 0.334

Gnomad4 AMR exome AF: 0.334

Gnomad4 ASJ exome AF: 0.463

Gnomad4 EAS exome AF: 0.161

Gnomad4 SAS exome AF: 0.491

Gnomad4 FIN exome AF: 0.325

Gnomad4 NFE exome AF: 0.448

Gnomad4 OTH exome AF: 0.421

GnomAD4 genome AF: 0.404 AC: 61441 AN: 151982 Hom.: 12934 Cov.: 33 AF XY: 0.403 AC XY: 29939 AN XY: 74270

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.428

Alfa AF: 0.436 Hom.: 14451

Bravo AF: 0.390

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 7 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	7.3
Dann	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs175049; hg19: chr14-75481368;