11-68309770-T-C

Position:

• chr11-68309770-T-C

Variant summary

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

The XM_011545029.2(LRP5):​c.118+10772T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,990 control chromosomes in the GnomAD database, including 49,685 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 0.81 (49685 hom., cov: 30)
• Consequence: LRP5 XM_011545029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

LRP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRP5	XM_011545029.2	c.118+10772T>C		intron_variant			XP_011543331.1
LRP5	XM_011545030.2	c.118+10772T>C		intron_variant			XP_011543332.1
LRP5	XM_011545031.2	c.118+10772T>C		intron_variant			XP_011543333.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122556 AN: 151872 Hom.: 49643 Cov.: 30

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.807 AC: 122648 AN: 151990 Hom.: 49685 Cov.: 30 AF XY: 0.804 AC XY: 59689 AN XY: 74284

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.825

Alfa AF: 0.805 Hom.: 46891

Bravo AF: 0.824

Asia WGS AF: 0.773 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312009; hg19: chr11-68077238;