rs4459385

Variant names:

• chr12-8457199-C-T
• rs4459385
• NM_001007033.2:c.32-699C>T

Variant summary

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

The NM_001007033.2(CLEC6A):​c.32-699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,004 control chromosomes in the GnomAD database, including 6,788 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 0.29 (6788 hom., cov: 31)
• Consequence: CLEC6A NM_001007033.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 4 publications found

Genes affected

CLEC6A (HGNC:14556): (C-type lectin domain containing 6A) The protein encoded by this gene is a type II membrane receptor with an extracellular C-type lectin-like domain fold. The extracellular portion binds structures with a high mannose content and has been shown to recognize several pathogens, including C. elegans, S. cerevisiae, M. tuberculosis, C. neoformans, and house dust mite. When stimulated, the encoded protein initiates signalling through the CARD9-Bcl10-Malt1 pathway, leading to the induction of cytokines. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC6A	NM_001007033.2	c.32-699C>T		intron_variant	Intron 1 of 5	ENST00000382073.4	NP_001007034.1
CLEC6A	NM_001317999.2	c.31+1057C>T		intron_variant	Intron 1 of 4		NP_001304928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC6A	ENST00000382073.4	c.32-699C>T		intron_variant	Intron 1 of 5	1	NM_001007033.2	ENSP00000371505.3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44588 AN: 151886 Hom.: 6778 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.294 AC: 44632 AN: 152004 Hom.: 6788 Cov.: 31 AF XY: 0.296 AC XY: 21972 AN XY: 74288

African (AFR) AF: 0.247 AC: 10216 AN: 41422

American (AMR) AF: 0.283 AC: 4319 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2454 AN: 5184

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3102 AN: 10544

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20888 AN: 67970

Other (OTH) AF: 0.284 AC: 599 AN: 2106

Alfa AF: 0.300 Hom.: 26100

Bravo AF: 0.288

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4459385; hg19: chr12-8609795;