rs4988327

chr11-68310198-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+11200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,226 control chromosomes in the GnomAD database, including 287 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 0.056 (287 hom., cov: 31)
• Consequence: LRP5 XM_011545029.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

LRP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP5	XM_011545029.2	c.118+11200A>G		intron_variant
LRP5	XM_011545030.2	c.118+11200A>G		intron_variant
LRP5	XM_011545031.2	c.118+11200A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0562 AC: 8550 AN: 152108 Hom.: 287 Cov.: 31

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0504

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0562 AC: 8558 AN: 152226 Hom.: 287 Cov.: 31 AF XY: 0.0546 AC XY: 4060 AN XY: 74418

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0504

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0369

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0679 Hom.: 68

Bravo AF: 0.0583

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4988327; hg19: chr11-68077666;