17-39928097-T-C

Variant names:

• chr17-39928097-T-C
• rs3744246
• NM_001195545.2:c.-175+283T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195545.2(LRRC3C):​c.-175+283T>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 152,206 control chromosomes in the GnomAD database, including 43,735 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 (43735 hom., cov: 34)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 42 publications found

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]

ENSG00000264968 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• 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 rank	MANE	Protein	UniProt
LRRC3C	NM_001195545.2	c.-175+283T>C		intron_variant	Intron 1 of 3	ENST00000377924.6	NP_001182474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC3C	ENST00000377924.6	c.-175+283T>C		intron_variant	Intron 1 of 3	3	NM_001195545.2	ENSP00000367157.4

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115103 AN: 152088 Hom.: 43726 Cov.: 34

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.757 AC: 115151 AN: 152206 Hom.: 43735 Cov.: 34 AF XY: 0.752 AC XY: 55961 AN XY: 74404

African (AFR) AF: 0.702 AC: 29125 AN: 41508

American (AMR) AF: 0.723 AC: 11065 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3809 AN: 5170

South Asian (SAS) AF: 0.775 AC: 3740 AN: 4828

European-Finnish (FIN) AF: 0.758 AC: 8038 AN: 10608

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54240 AN: 68010

Other (OTH) AF: 0.762 AC: 1611 AN: 2114

Alfa AF: 0.782 Hom.: 193134

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	-0.80
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		0.084
PromoterAI		0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3744246; hg19: chr17-38084350;