rs4794820

chr17-39933091-A-Gchr17-39933091-A-T

Variant summary

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

The NM_001195545.2(LRRC3C):c.-174-2711A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,788 control chromosomes in the GnomAD database, including 22,771 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 0.55 (22771 hom., cov: 31)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

Genes affected

LRRC3C (HGNC:40034): (leucine rich repeat containing 3C) Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC3C	NM_001195545.2	c.-174-2711A>G		intron_variant		ENST00000377924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-174-2711A>G		intron_variant		3	NM_001195545.2	P1
	ENST00000582263.1	n.162-1520A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82829 AN: 151670 Hom.: 22775 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.546 AC: 82840 AN: 151788 Hom.: 22771 Cov.: 31 AF XY: 0.544 AC XY: 40367 AN XY: 74168

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.556

Alfa AF: 0.552 Hom.: 10187

Bravo AF: 0.554

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4794820; hg19: chr17-38089344;