dbSNP rs3781701: LRRC32:c.*1229C>T (chr11-76658375-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

14 publications found

Variant links:

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]

LRRC32 Gene-Disease associations (from GenCC):

cleft palate, proliferative retinopathy, and developmental delay
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

LRRC32 links:

ENSG00000236304 (HGNC:58233):

ENSG00000236304 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LRRC32	NM_001128922.2 link	c.*1229C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000260061.9	NP_001122394.1	Q14392A0A024R5J7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC32	ENST00000260061.9 link	c.*1229C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001128922.2	ENSP00000260061.5		Q14392

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50973

AN:

152076

Hom.:

8686

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.335

AC XY:

174

AN XY:

520

show subpopulations

African (AFR)

AF:

0.429

AC:

AN:

American (AMR)

AF:

0.400

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AF:

0.375

AC:

AN:

European-Finnish (FIN)

AF:

0.339

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.318

AC:

163

AN:

512

Other (OTH)

AF:

0.304

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.335

AC:

50984

AN:

152196

Hom.:

8683

Cov.:

AF XY:

0.335

AC XY:

24957

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.292

AC:

12143

AN:

41540

American (AMR)

AF:

0.356

AC:

5445

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

961

AN:

3470

East Asian (EAS)

AF:

0.350

AC:

1807

AN:

5156

South Asian (SAS)

AF:

0.360

AC:

1738

AN:

4828

European-Finnish (FIN)

AF:

0.384

AC:

4073

AN:

10600

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.349

AC:

23714

AN:

67998

Other (OTH)

AF:

0.319

AC:

674

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1807

3615

5422

7230

9037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.339

Hom.:

37673

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

(source)

DANN

Benign

0.50

PhyloP100

-0.058

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over