rs7753340

chr6-149856312-T-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• 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/exons	MANE	UniProt
LRP11	NM_032832.6	c.614-3152A>T		intron_variant		ENST00000239367.7
RAET1E-LRP11	NR_182438.1	n.2514-3152A>T		intron_variant, non_coding_transcript_variant
LRP11	NM_001410946.1	c.614-3152A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRP11	ENST00000239367.7	c.614-3152A>T		intron_variant		1	NM_032832.6	P1
LRP11	ENST00000367368.3	c.614-3152A>T		intron_variant		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

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00897

Gnomad4 OTH AF: 0.101

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753340; hg19: chr6-150177448;