rs8079416

Positions:

• chr17-39936460-T-C
• chr17-39936460-T-G

Variant summary

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

The NM_001195545.2(LRRC3C):​c.-82+566T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,620 control chromosomes in the GnomAD database, including 15,862 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 0.46 (15862 hom., cov: 30)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC3C	NM_001195545.2	c.-82+566T>C		intron_variant		ENST00000377924.6
LRRC3C	XM_017024003.1	c.-82+566T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-82+566T>C		intron_variant		3	NM_001195545.2	P1
	ENST00000582263.1	n.368+566T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69053 AN: 151502 Hom.: 15863 Cov.: 30

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.456 AC: 69072 AN: 151620 Hom.: 15862 Cov.: 30 AF XY: 0.452 AC XY: 33491 AN XY: 74094

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.458

Alfa AF: 0.458 Hom.: 32832

Bravo AF: 0.474

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8079416; hg19: chr17-38092713;