rs3901533

Positions:

• chr12-10124484-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_197947.3(CLEC7A):​c.492+813T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,032 control chromosomes in the GnomAD database, including 34,317 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 0.66 (34317 hom., cov: 31)
• Consequence: CLEC7A NM_197947.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

Genes affected

CLEC7A (HGNC:14558): (C-type lectin domain containing 7A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. The encoded glycoprotein is a small type II membrane receptor with an extracellular C-type lectin-like domain fold and a cytoplasmic domain with an immunoreceptor tyrosine-based activation motif. It functions as a pattern-recognition receptor that recognizes a variety of beta-1,3-linked and beta-1,6-linked glucans from fungi and plants, and in this way plays a role in innate immune response. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]

LOC105369655 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC7A	NM_197947.3	c.492+813T>G		intron_variant		ENST00000304084.13
LOC105369655	XR_007063208.1	n.182-6597A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC7A	ENST00000304084.13	c.492+813T>G		intron_variant		1	NM_197947.3	P4

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99615 AN: 151914 Hom.: 34307 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.655 AC: 99655 AN: 152032 Hom.: 34317 Cov.: 31 AF XY: 0.650 AC XY: 48259 AN XY: 74294

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.681

Alfa AF: 0.741 Hom.: 53315

Bravo AF: 0.640

Asia WGS AF: 0.299 AC: 1039 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.42

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

Publications

LitVar

Other links and lift over

dbSNP: rs3901533; hg19: chr12-10277083;