Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128922.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LRRC32	NM_001128922.2	MANE Select	c.*1229C>T	3_prime_UTR	Exon 3 of 3	NP_001122394.1
LRRC32	NM_005512.3		c.*1229C>T	3_prime_UTR	Exon 3 of 3	NP_005503.1
LRRC32	NM_001370189.1		c.*1229C>T	3_prime_UTR	Exon 3 of 3	NP_001357118.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LRRC32	ENST00000260061.9	TSL:1 MANE Select	c.*1229C>T	3_prime_UTR	Exon 3 of 3	ENSP00000260061.5
LRRC32	ENST00000407242.6	TSL:1	c.*1229C>T	3_prime_UTR	Exon 3 of 3	ENSP00000384126.2
ENSG00000236304	ENST00000447519.2	TSL:1	n.173+1219G>A	intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over