11-68311851-A-G

Position:

• chr11-68311851-A-G

Variant summary

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

The XM_011545029.2(LRP5):​c.118+12853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,188 control chromosomes in the GnomAD database, including 7,529 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 0.29 (7529 hom., cov: 32)
• Consequence: LRP5 XM_011545029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

LRP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP5	XM_011545029.2	c.118+12853A>G		intron_variant
LRP5	XM_011545030.2	c.118+12853A>G		intron_variant
LRP5	XM_011545031.2	c.118+12853A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44535 AN: 152070 Hom.: 7524 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.293 AC: 44559 AN: 152188 Hom.: 7529 Cov.: 32 AF XY: 0.301 AC XY: 22417 AN XY: 74400

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.331

Alfa AF: 0.288 Hom.: 1733

Bravo AF: 0.298

Asia WGS AF: 0.505 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs682429; hg19: chr11-68079319;