rs10762360

chr10-70299750-G-Cchr10-70299750-G-T

Variant summary

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

The NM_001278212.2(LRRC20):c.*1604C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,842 control chromosomes in the GnomAD database, including 37,733 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 0.70 (37505 hom., cov: 31)
  • Exomes 𝑓: 0.74 (228 hom.)
• Consequence: LRRC20 NM_001278212.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC20	NM_001278212.2	c.*1604C>G		3_prime_UTR_variant	5/5	ENST00000446961.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC20	ENST00000446961.4	c.*1604C>G		3_prime_UTR_variant	5/5	2	NM_001278212.2	P1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106146 AN: 151924 Hom.: 37483 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.745 AC: 596 AN: 800 Hom.: 228 Cov.: 0 AF XY: 0.741 AC XY: 461 AN XY: 622

Gnomad4 AFR exome AF: 0.722

Gnomad4 AMR exome AF: 0.417

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.412

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.760

Gnomad4 OTH exome AF: 0.794

GnomAD4 genome AF: 0.699 AC: 106215 AN: 152042 Hom.: 37505 Cov.: 31 AF XY: 0.699 AC XY: 51954 AN XY: 74332

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.670

Alfa AF: 0.726 Hom.: 5049

Bravo AF: 0.681

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.4
Dann	Benign	0.73

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: rs10762360; hg19: chr10-72059506;