rs11020802

chr11-94493959-C-Achr11-94493959-C-Gchr11-94493959-C-T

Variant summary

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

The XM_011542837.3(MRE11):c.-105-1053G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,126 control chromosomes in the GnomAD database, including 7,787 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.31 (7782 hom., cov: 33)
  • Exomes 𝑓: 0.35 (5 hom.)
• Consequence: MRE11 XM_011542837.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.45

Genes affected

MRE11 (HGNC:):

ANKRD49 (HGNC:25970): (ankyrin repeat domain 49) Involved in positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 11-94493959-C-A is Benign according to our data. Variant chr11-94493959-C-A is described in ClinVar as [Benign]. Clinvar id is 1291079.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRE11	XM_011542837.3	c.-105-1053G>T		intron_variant
ANKRD49	NM_017704.3			upstream_gene_variant		ENST00000544612.6
ANKRD49	XM_017017941.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD49	ENST00000544612.6			upstream_gene_variant		1	NM_017704.3	P1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47343 AN: 151946 Hom.: 7782 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.350 AC: 21 AN: 60 Hom.: 5 Cov.: 0 AF XY: 0.348 AC XY: 16 AN XY: 46

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.385

GnomAD4 genome AF: 0.311 AC: 47348 AN: 152066 Hom.: 7782 Cov.: 33 AF XY: 0.317 AC XY: 23562 AN XY: 74328

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.333

Alfa AF: 0.173 Hom.: 350

Bravo AF: 0.307

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

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	0.094
Dann	Benign	0.53

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: rs11020802; hg19: chr11-94227125; COSMIC: COSV57060822; COSMIC: COSV57060822;