rs9371201

Variant names:

• chr6-149823865-C-T
• rs9371201
• NM_032832.6:c.1348+2399G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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]

ENSG00000285991 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRP11	NM_032832.6	c.1348+2399G>A		intron_variant	Intron 6 of 6	ENST00000239367.7	NP_116221.3
RAET1E-LRP11	NR_182438.1	n.3248+2399G>A		intron_variant	Intron 14 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP11	ENST00000239367.7	c.1348+2399G>A		intron_variant	Intron 6 of 6	1	NM_032832.6	ENSP00000239367.2
ENSG00000285991	ENST00000647612.1	n.*1234+2399G>A		intron_variant	Intron 14 of 14			ENSP00000498179.1
ENSG00000285889	ENST00000628047.1	n.31+2399G>A		intron_variant	Intron 1 of 1	5

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

African (AFR) AF: 0.166 AC: 6875 AN: 41442

American (AMR) AF: 0.452 AC: 6897 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2542 AN: 5154

South Asian (SAS) AF: 0.317 AC: 1519 AN: 4796

European-Finnish (FIN) AF: 0.371 AC: 3905 AN: 10528

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23012 AN: 67938

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.333 Hom.: 27299

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
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9371201; hg19: chr6-150145001;