rs8079416

Variant names:

• chr17-39936460-T-C
• rs8079416
• NM_001195545.2:c.-82+566T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-39936460-T-C
• chr17-39936460-T-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.-82+566T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,620 control chromosomes in the GnomAD database, including 15,862 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 (15862 hom., cov: 30)
• Consequence: LRRC3C NM_001195545.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 43 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC3C	NM_001195545.2	MANE Select	c.-82+566T>C		intron	N/A	NP_001182474.1	A6NJW4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC3C	ENST00000377924.6	TSL:3 MANE Select	c.-82+566T>C		intron	N/A	ENSP00000367157.4	A6NJW4
	ENSG00000264968	ENST00000582263.1	TSL:5	n.368+566T>C		intron	N/A
	ENSG00000264968	ENST00000790964.1		n.23-2878T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69053 AN: 151502 Hom.: 15863 Cov.: 30

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.456 AC: 69072 AN: 151620 Hom.: 15862 Cov.: 30 AF XY: 0.452 AC XY: 33491 AN XY: 74094

African (AFR) AF: 0.445 AC: 18361 AN: 41266

American (AMR) AF: 0.497 AC: 7570 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3462

East Asian (EAS) AF: 0.565 AC: 2913 AN: 5160

South Asian (SAS) AF: 0.453 AC: 2171 AN: 4788

European-Finnish (FIN) AF: 0.364 AC: 3824 AN: 10514

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31195 AN: 67890

Other (OTH) AF: 0.458 AC: 962 AN: 2102

Alfa AF: 0.459 Hom.: 48728

Bravo AF: 0.474

Asia WGS AF: 0.467 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs8079416; hg19: chr17-38092713;