rs3219463

chr1-45340760-C-T

Variant summary

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

The NM_025077.4(TOE1):c.53-313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,990 control chromosomes in the GnomAD database, including 5,839 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (5839 hom., cov: 31)
• Consequence: TOE1 NM_025077.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.367

Genes affected

TOE1 (HGNC:15954): (target of EGR1, exonuclease) Enables poly(A)-specific ribonuclease activity and snRNA binding activity. Involved in RNA phosphodiester bond hydrolysis, exonucleolytic and snRNA 3'-end processing. Located in Cajal body and cytoplasm. Implicated in pontocerebellar hypoplasia type 7. [provided by Alliance of Genome Resources, Apr 2022]

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 Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 1-45340760-C-T is Benign according to our data. Variant chr1-45340760-C-T is described in ClinVar as [Benign]. Clinvar id is 1221523.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TOE1	NM_025077.4	c.53-313C>T		intron_variant		ENST00000372090.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TOE1	ENST00000372090.6	c.53-313C>T		intron_variant		1	NM_025077.4	P1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40947 AN: 151872 Hom.: 5808 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.296

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.270 AC: 41025 AN: 151990 Hom.: 5839 Cov.: 31 AF XY: 0.269 AC XY: 20002 AN XY: 74290

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.302

Alfa AF: 0.253 Hom.: 826

Bravo AF: 0.288

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.6
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3219463; hg19: chr1-45806432;