rs7753340

Variant names:

• chr6-149856312-T-A
• rs7753340
• NM_032832.6:c.614-3152A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032832.6(LRP11):​c.614-3152A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,208 control chromosomes in the GnomAD database, including 2,430 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 0.11 (2430 hom., cov: 32)
• Consequence: LRP11 NM_032832.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRP11	NM_032832.6	c.614-3152A>T		intron_variant	Intron 1 of 6	ENST00000239367.7	NP_116221.3
LRP11	NM_001410946.1	c.614-3152A>T		intron_variant	Intron 1 of 3		NP_001397875.1
RAET1E-LRP11	NR_182438.1	n.2514-3152A>T		intron_variant	Intron 9 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRP11	ENST00000239367.7	c.614-3152A>T		intron_variant	Intron 1 of 6	1	NM_032832.6	ENSP00000239367.2
ENSG00000285991	ENST00000647612.1	n.*500-3152A>T		intron_variant	Intron 9 of 14			ENSP00000498179.1
LRP11	ENST00000367368.3	c.614-3152A>T		intron_variant	Intron 1 of 3	2		ENSP00000356338.2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16331 AN: 152090 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00897

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.108 AC: 16408 AN: 152208 Hom.: 2430 Cov.: 32 AF XY: 0.108 AC XY: 8011 AN XY: 74434

African (AFR) AF: 0.338 AC: 14012 AN: 41458

American (AMR) AF: 0.0478 AC: 732 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3468

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5182

South Asian (SAS) AF: 0.124 AC: 597 AN: 4824

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10622

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.00897 AC: 610 AN: 68030

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0630 Hom.: 165

Bravo AF: 0.118

Asia WGS AF: 0.107 AC: 373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7753340; hg19: chr6-150177448;