rs11595603

Positions:

• chr10-70380313-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278212.2(LRRC20):​c.-64+2236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,218 control chromosomes in the GnomAD database, including 256 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 0.050 (256 hom., cov: 32)
• Consequence: LRRC20 NM_001278212.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870

Genes affected

LRRC20 (HGNC:23421): (leucine rich repeat containing 20)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC20	NM_001278212.2	c.-64+2236G>A		intron_variant		ENST00000446961.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC20	ENST00000446961.4	c.-64+2236G>A		intron_variant		2	NM_001278212.2	P1

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7592 AN: 152100 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.0541

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0499 AC: 7598 AN: 152218 Hom.: 256 Cov.: 32 AF XY: 0.0500 AC XY: 3719 AN XY: 74434

Gnomad4 AFR AF: 0.0700

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0424 Hom.: 29

Bravo AF: 0.0505

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.58

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: rs11595603; hg19: chr10-72140069;