rs10831234

Positions:

• chr11-94500021-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011542837.3(MRE11):​c.-105-7115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,208 control chromosomes in the GnomAD database, including 1,114 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1114 hom., cov: 32)
• Consequence: MRE11 XM_011542837.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

MRE11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRE11	XM_011542837.3	c.-105-7115G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17345 AN: 152090 Hom.: 1112 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.114 AC: 17363 AN: 152208 Hom.: 1114 Cov.: 32 AF XY: 0.114 AC XY: 8512 AN XY: 74420

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0938

Gnomad4 OTH AF: 0.105

Alfa AF: 0.107 Hom.: 187

Bravo AF: 0.116

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10831234; hg19: chr11-94233187;