rs3781701

Positions:

• chr11-76658375-G-A
• chr11-76658375-G-C
• chr11-76658375-G-T

Variant summary

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

The NM_001128922.2(LRRC32):​c.*1229C>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 0.335 in 152,914 control chromosomes in the GnomAD database, including 8,732 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 0.33 (8683 hom., cov: 33)
  • Exomes 𝑓: 0.32 (49 hom.)
• Consequence: LRRC32 NM_001128922.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC32	NM_001128922.2	c.*1229C>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.*1229C>T		3_prime_UTR_variant	3/3	1	NM_001128922.2	ENSP00000260061.5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50973 AN: 152076 Hom.: 8686 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.322 AC: 231 AN: 718 Hom.: 49 Cov.: 0 AF XY: 0.335 AC XY: 174 AN XY: 520

Gnomad4 AFR exome AF: 0.429

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.375

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.318

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.335 AC: 50984 AN: 152196 Hom.: 8683 Cov.: 33 AF XY: 0.335 AC XY: 24957 AN XY: 74416

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.319

Alfa AF: 0.339 Hom.: 17838

Bravo AF: 0.330

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.50

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: rs3781701; hg19: chr11-76369419;