rs4795404

chr17-39929538-A-Cchr17-39929538-A-Gchr17-39929538-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.-175+1724A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,090 control chromosomes in the GnomAD database, including 43,691 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 0.76 (43683 hom., cov: 32)
  • Exomes 𝑓: 0.94 (8 hom.)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC3C	NM_001195545.2	c.-175+1724A>C		intron_variant		ENST00000377924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-175+1724A>C		intron_variant		3	NM_001195545.2	P1
	ENST00000582263.1	n.161+305A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114993 AN: 151954 Hom.: 43673 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.944 AC: 17 AN: 18 Hom.: 8 AF XY: 1.00 AC XY: 6 AN XY: 6

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.900

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.756 AC: 115042 AN: 152072 Hom.: 43683 Cov.: 32 AF XY: 0.752 AC XY: 55907 AN XY: 74342

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.762

Alfa AF: 0.779 Hom.: 9502

Bravo AF: 0.754

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.87
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4795404; hg19: chr17-38085791;