17-39938921-G-C

Variant summary

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

The NM_001195545.2(LRRC3C):c.-81-2522G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,566 control chromosomes in the GnomAD database, including 15,835 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 (15835 hom., cov: 28)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC3C	NM_001195545.2	c.-81-2522G>C		intron_variant		ENST00000377924.6
LRRC3C	XM_017024003.1	c.-81-2522G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-81-2522G>C		intron_variant		3	NM_001195545.2	P1
	ENST00000582263.1	n.369-417G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69001 AN: 151448 Hom.: 15836 Cov.: 28

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.455 AC: 69021 AN: 151566 Hom.: 15835 Cov.: 28 AF XY: 0.452 AC XY: 33483 AN XY: 74082

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.455

Alfa AF: 0.293 Hom.: 659

Bravo AF: 0.473

Asia WGS AF: 0.461 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6503525; hg19: chr17-38095174;