rs7944357

chr11-76662995-A-G

Variant summary

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

The NM_001128922.2(LRRC32):c.85-1487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 152,138 control chromosomes in the GnomAD database, including 26,532 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 0.59 (26497 hom., cov: 31)
  • Exomes 𝑓: 0.60 (35 hom.)
• Consequence: LRRC32 NM_001128922.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

LRRC32 (HGNC:4161): (leucine rich repeat containing 32) This gene encodes a type I membrane protein which contains 20 leucine-rich repeats. Alterations in the chromosomal region 11q13-11q14 are involved in several pathologies. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC32	NM_001128922.2	c.85-1487T>C		intron_variant		ENST00000260061.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC32	ENST00000260061.9	c.85-1487T>C		intron_variant		1	NM_001128922.2	P1
	ENST00000447519.2	n.627A>G		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89047 AN: 151834 Hom.: 26469 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.605

GnomAD4 exome AF: 0.602 AC: 112 AN: 186 Hom.: 35 Cov.: 0 AF XY: 0.597 AC XY: 74 AN XY: 124

Gnomad4 AFR exome AF: 0.250

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.667

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.635

Gnomad4 OTH exome AF: 0.429

GnomAD4 genome AF: 0.586 AC: 89119 AN: 151952 Hom.: 26497 Cov.: 31 AF XY: 0.588 AC XY: 43658 AN XY: 74274

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.605

Alfa AF: 0.576 Hom.: 24395

Bravo AF: 0.587

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.1
Dann	Benign	0.75

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: rs7944357; hg19: chr11-76374039;