dbSNP rs11060167: LRRC43:p.Arg330Arg (chr12-122191466-A-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001098519.2(LRRC43):c.988A>C(p.Arg330Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,613,684 control chromosomes in the GnomAD database, including 66,090 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 0.23 ( 5110 hom., cov: 31)

Exomes 𝑓: 0.28 ( 60980 hom. )

Consequence

LRRC43
NM_001098519.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.01

Publications

20 publications found

Variant links:

Genes affected

LRRC43 (HGNC:28562): (leucine rich repeat containing 43)

LRRC43 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP7

Synonymous conserved (PhyloP=3.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC43	NM_001098519.2 link	c.988A>C	p.Arg330Arg	synonymous_variant	Exon 6 of 12	ENST00000339777.5	NP_001091989.1	Q8N309-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
LRRC43	ENST00000339777.5 link	c.988A>C	p.Arg330Arg	synonymous_variant	Exon 6 of 12	5	NM_001098519.2	ENSP00000344233.4	Q8N309-1
LRRC43	ENST00000537729.5 link	c.433A>C	p.Arg145Arg	synonymous_variant	Exon 6 of 6	5		ENSP00000438751.1	F5H0N3
LRRC43	ENST00000541498.5 link	n.430+6687A>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34967

AN:

151878

Hom.:

5113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.711

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.260

Gnomad OTH

AF:

0.216

GnomAD2 exomes

AF:

0.287

AC:

71486

AN:

249480

AF XY:

0.290

show subpopulations

Gnomad AFR exome

AF:

0.0985

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.713

Gnomad FIN exome

AF:

0.325

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.277

AC:

404366

AN:

1461686

Hom.:

60980

Cov.:

AF XY:

0.278

AC XY:

202064

AN XY:

727148

show subpopulations

African (AFR)

AF:

0.0957

AC:

3204

AN:

33480

American (AMR)

AF:

0.205

AC:

9171

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

5839

AN:

26134

East Asian (EAS)

AF:

0.700

AC:

27796

AN:

39694

South Asian (SAS)

AF:

0.307

AC:

26483

AN:

86242

European-Finnish (FIN)

AF:

0.324

AC:

17322

AN:

53414

Middle Eastern (MID)

AF:

0.193

AC:

1110

AN:

5764

European-Non Finnish (NFE)

AF:

0.267

AC:

296876

AN:

1111856

Other (OTH)

AF:

0.274

AC:

16565

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

14929

29858

44788

59717

74646

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10142

20284

30426

40568

50710

<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:

0.230

AC:

34970

AN:

151998

Hom.:

5110

Cov.:

AF XY:

0.239

AC XY:

17737

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.100

AC:

4161

AN:

41500

American (AMR)

AF:

0.194

AC:

2959

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

777

AN:

3468

East Asian (EAS)

AF:

0.710

AC:

3652

AN:

5146

South Asian (SAS)

AF:

0.316

AC:

1519

AN:

4814

European-Finnish (FIN)

AF:

0.335

AC:

3539

AN:

10562

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.260

AC:

17664

AN:

67930

Other (OTH)

AF:

0.219

AC:

462

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1296

2591

3887

5182

6478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<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:

0.234

Hom.:

2558

Bravo

AF:

0.215

Asia WGS

AF:

0.431

AC:

1498

AN:

3478

EpiCase

AF:

0.251

EpiControl

AF:

0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.2

(source)

DANN

Benign

0.48

PhyloP100

3.0

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