dbSNP rs7944357: LRRC32:c.85-1487T>C (chr11-76662995-A-G) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

Publications

9 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:

LRRC32-AS1 (HGNC:58233):

LRRC32-AS1 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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	UniProt
LRRC32	NM_001128922.2	MANE Select	c.85-1487T>C	intron	N/A	NP_001122394.1	Q14392
LRRC32	NM_001370187.1		c.85-1487T>C	intron	N/A	NP_001357116.1	Q14392
LRRC32	NM_001370188.1		c.85-1487T>C	intron	N/A	NP_001357117.1	Q14392

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LRRC32	ENST00000260061.9	TSL:1 MANE Select	c.85-1487T>C	intron	N/A	ENSP00000260061.5	Q14392
LRRC32	ENST00000407242.6	TSL:1	c.85-1487T>C	intron	N/A	ENSP00000384126.2	Q14392
LRRC32	ENST00000421973.1	TSL:1	c.85-1487T>C	intron	N/A	ENSP00000413331.1	C9JYU3

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

89047

AN:

151834

Hom.:

26469

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.597

AC XY:

AN XY:

124

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.667

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.531

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.635

AC:

AN:

126

Other (OTH)

AF:

0.429

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

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:

0.586

AC:

89119

AN:

151952

Hom.:

26497

Cov.:

AF XY:

0.588

AC XY:

43658

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.652

AC:

27013

AN:

41428

American (AMR)

AF:

0.560

AC:

8555

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.646

AC:

2241

AN:

3468

East Asian (EAS)

AF:

0.329

AC:

1690

AN:

5134

South Asian (SAS)

AF:

0.579

AC:

2788

AN:

4816

European-Finnish (FIN)

AF:

0.562

AC:

5935

AN:

10562

Middle Eastern (MID)

AF:

0.609

AC:

179

AN:

294

European-Non Finnish (NFE)

AF:

0.569

AC:

38657

AN:

67958

Other (OTH)

AF:

0.605

AC:

1275

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1904

3808

5713

7617

9521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.577

Hom.:

66328

Bravo

AF:

0.587

Asia WGS

AF:

0.501

AC:

1746

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.1

(source)

DANN

Benign

0.75

PhyloP100

0.15

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