rs11060167

chr12-122191466-A-Cchr12-122191466-A-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001098519.2(LRRC43):c.988A>C(p.Arg330=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.01

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LRRC43	NM_001098519.2	c.988A>C	p.Arg330=	synonymous_variant	6/12	ENST00000339777.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC43	ENST00000339777.5	c.988A>C	p.Arg330=	synonymous_variant	6/12	5	NM_001098519.2	P1
LRRC43	ENST00000537729.5	c.433A>C	p.Arg145=	synonymous_variant	6/6	5
LRRC43	ENST00000541498.5	n.430+6687A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34967 AN: 151878 Hom.: 5113 Cov.: 31

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

GnomAD3 exomes AF: 0.287 AC: 71486 AN: 249480 Hom.: 12487 AF XY: 0.290 AC XY: 39246 AN XY: 135354

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 SAS exome AF: 0.309

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.: 35 AF XY: 0.278 AC XY: 202064 AN XY: 727148

Gnomad4 AFR exome AF: 0.0957

Gnomad4 AMR exome AF: 0.205

Gnomad4 ASJ exome AF: 0.223

Gnomad4 EAS exome AF: 0.700

Gnomad4 SAS exome AF: 0.307

Gnomad4 FIN exome AF: 0.324

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.230 AC: 34970 AN: 151998 Hom.: 5110 Cov.: 31 AF XY: 0.239 AC XY: 17737 AN XY: 74292

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.219

Alfa AF: 0.235 Hom.: 2556

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
Dann	Benign	0.48

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: rs11060167; hg19: chr12-122676013;