rs9371201

chr6-149823865-C-T

Variant summary

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

The NM_032832.6(LRP11):c.1348+2399G>A 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 151,886 control chromosomes in the GnomAD database, including 8,272 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 0.31 (8272 hom., cov: 31)
• Consequence: LRP11 NM_032832.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LRP11 (HGNC:16936): (LDL receptor related protein 11) Enables phosphoprotein binding activity. Predicted to act upstream of or within several processes, including response to cold; response to immobilization stress; and response to water deprivation. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RAET1E-LRP11 (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 (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRP11	NM_032832.6	c.1348+2399G>A		intron_variant		ENST00000239367.7
RAET1E-LRP11	NR_182438.1	n.3248+2399G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP11	ENST00000239367.7	c.1348+2399G>A		intron_variant		1	NM_032832.6	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47242 AN: 151768 Hom.: 8261 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.311 AC: 47263 AN: 151886 Hom.: 8272 Cov.: 31 AF XY: 0.316 AC XY: 23485 AN XY: 74216

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.335

Alfa AF: 0.342 Hom.: 18421

Bravo AF: 0.316

Asia WGS AF: 0.357 AC: 1242 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	3.0
Dann	Benign	0.69

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: rs9371201; hg19: chr6-150145001;