NM_001195545.2:c.-174-2711A>G

Variant names:

• chr17-39933091-A-G
• rs4794820
• NM_001195545.2:c.-174-2711A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 56 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=-0.88).
• 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 rank	MANE	Protein	UniProt
LRRC3C	NM_001195545.2	c.-174-2711A>G		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.-174-2711A>G		intron_variant	Intron 1 of 3	3	NM_001195545.2	ENSP00000367157.4
ENSG00000264968	ENST00000582263.1	n.162-1520A>G		intron_variant	Intron 2 of 4	5
ENSG00000264968	ENST00000790964.1	n.22+5190A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.490 AC: 20252 AN: 41318

American (AMR) AF: 0.577 AC: 8803 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3729 AN: 5178

South Asian (SAS) AF: 0.587 AC: 2818 AN: 4802

European-Finnish (FIN) AF: 0.506 AC: 5312 AN: 10502

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38438 AN: 67946

Other (OTH) AF: 0.556 AC: 1173 AN: 2110

Alfa AF: 0.558 Hom.: 49140

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4794820; hg19: chr17-38089344;