chr11-94471764-A-C

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 5 ACMG points: 6P and 1B. PM2PP3_StrongBP6

The NM_005591.4(MRE11):c.660-5T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,455,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

MRE11
NM_005591.4 splice_region, intron

Scores

Splicing: ADA: 1.000

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:1

Conservation

PhyloP100: -0.0330

Publications

1 publications found

Variant links:

Genes affected

MRE11 (HGNC:7230): (MRE11 homolog, double strand break repair nuclease) This gene encodes a nuclear protein involved in homologous recombination, telomere length maintenance, and DNA double-strand break repair. By itself, the protein has 3' to 5' exonuclease activity and endonuclease activity. The protein forms a complex with the RAD50 homolog; this complex is required for nonhomologous joining of DNA ends and possesses increased single-stranded DNA endonuclease and 3' to 5' exonuclease activities. In conjunction with a DNA ligase, this protein promotes the joining of noncomplementary ends in vitro using short homologies near the ends of the DNA fragments. This gene has a pseudogene on chromosome 3. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

MRE11 Gene-Disease associations (from GenCC):

ataxia-telangiectasia-like disorder 1
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet, Ambry Genetics
breast cancer
Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
familial ovarian cancer
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
hereditary breast carcinoma
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
prostate cancer
Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics

MRE11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.

BP6

Variant 11-94471764-A-C is Benign according to our data. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607. Variant chr11-94471764-A-C is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 141607.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRE11	NM_005591.4 link	c.660-5T>G		splice_region_variant, intron_variant	Intron 7 of 19	ENST00000323929.8	NP_005582.1	P49959-1A0A024R395

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MRE11	ENST00000323929.8 link	c.660-5T>G	splice_region_variant, intron_variant	Intron 7 of 19	1	NM_005591.4	ENSP00000325863.4	P49959-1
MRE11	ENST00000323977.7 link	c.660-5T>G	splice_region_variant, intron_variant	Intron 7 of 18	1		ENSP00000326094.3	P49959-2
MRE11	ENST00000407439.7 link	c.669-5T>G	splice_region_variant, intron_variant	Intron 7 of 19	2		ENSP00000385614.3	P49959-3
MRE11	ENST00000393241.8 link	c.660-5T>G	splice_region_variant, intron_variant	Intron 7 of 19	5		ENSP00000376933.4	F8W7U8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000275

AC:

AN:

1455400

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

724042

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33288

American (AMR)

AF:

0.00

AC:

AN:

44340

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25994

East Asian (EAS)

AF:

0.00

AC:

AN:

39530

South Asian (SAS)

AF:

0.00

AC:

AN:

85840

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52962

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5628

European-Non Finnish (NFE)

AF:

0.00000361

AC:

AN:

1107760

Other (OTH)

AF:

0.00

AC:

AN:

60058

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000180

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Ataxia-telangiectasia-like disorder 1

Uncertain:1

Feb 15, 2024

Fulgent Genetics, Fulgent Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary cancer-predisposing syndrome

Uncertain:1

Apr 19, 2023

Ambry Genetics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.660-5T>G intronic variant results from a T to G substitution 5 nucleotides upstream from coding exon 7 in the MRE11A gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Ataxia-telangiectasia-like disorder

Benign:1

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

-0.033

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=25/75

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.96

SpliceAI score (max)

0.36

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.25

Position offset: -1

DS_AL_spliceai

0.36

Position offset: -5

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over