rs7309123

chr12-10119994-G-C

Variant summary

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

The NM_197947.3(CLEC7A):c.612-1404C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,944 control chromosomes in the GnomAD database, including 16,680 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 0.42 (16680 hom., cov: 32)
• Consequence: CLEC7A NM_197947.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC7A	NM_197947.3	c.612-1404C>G		intron_variant		ENST00000304084.13
LOC105369655	XR_007063208.1	n.181+4451G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC7A	ENST00000304084.13	c.612-1404C>G		intron_variant		1	NM_197947.3	P4

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64536 AN: 151826 Hom.: 16682 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.425 AC: 64530 AN: 151944 Hom.: 16680 Cov.: 32 AF XY: 0.423 AC XY: 31394 AN XY: 74276

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.483

Alfa AF: 0.500 Hom.: 2632

Bravo AF: 0.408

Asia WGS AF: 0.233 AC: 813 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.72

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: rs7309123; hg19: chr12-10272593;