11-76657978-G-A

Position:

• chr11-76657978-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001128922.2(LRRC32):​c.*1626C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 152,464 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.010 (19 hom., cov: 33)
  • Exomes 𝑓: 0.0063 (0 hom.)
• Consequence: LRRC32 NM_001128922.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.35

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]

ENSG00000236304 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-76657978-G-A is Benign according to our data. Variant chr11-76657978-G-A is described in ClinVar as [Benign]. Clinvar id is 1879212.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC32	NM_001128922.2	c.*1626C>T		3_prime_UTR_variant	3/3	ENST00000260061.9	NP_001122394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC32	ENST00000260061	c.*1626C>T		3_prime_UTR_variant	3/3	1	NM_001128922.2	ENSP00000260061.5

Frequencies

GnomAD3 genomes AF: 0.0105 AC: 1595 AN: 152188 Hom.: 19 Cov.: 33

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.00641

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00703

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0110

GnomAD4 exome AF: 0.00633 AC: 1 AN: 158 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 86

Gnomad4 EAS exome AF: 0.00725

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0105 AC: 1595 AN: 152306 Hom.: 19 Cov.: 33 AF XY: 0.0105 AC XY: 781 AN XY: 74466

Gnomad4 AFR AF: 0.00229

Gnomad4 AMR AF: 0.00641

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0150

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0132 Hom.: 1

Bravo AF: 0.00965

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2023

LRRC32: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.68

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: rs149032268; hg19: chr11-76369022;