NM_001195545.2:c.-81-2522G>C

Variant names:

• chr17-39938921-G-C
• rs6503525
• NM_001195545.2:c.-81-2522G>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.-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
• Publications: 38 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195545.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC3C	NM_001195545.2	MANE Select	c.-81-2522G>C		intron	N/A	NP_001182474.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC3C	ENST00000377924.6	TSL:3 MANE Select	c.-81-2522G>C		intron	N/A	ENSP00000367157.4
	ENSG00000264968	ENST00000582263.1	TSL:5	n.369-417G>C		intron	N/A
	ENSG00000264968	ENST00000790964.1		n.23-417G>C		intron	N/A

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

African (AFR) AF: 0.446 AC: 18421 AN: 41262

American (AMR) AF: 0.498 AC: 7577 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1526 AN: 3464

East Asian (EAS) AF: 0.545 AC: 2806 AN: 5152

South Asian (SAS) AF: 0.452 AC: 2165 AN: 4788

European-Finnish (FIN) AF: 0.368 AC: 3865 AN: 10510

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31154 AN: 67870

Other (OTH) AF: 0.455 AC: 955 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs6503525; hg19: chr17-38095174;