chr12-10119994-G-C

Variant names:

• chr12-10119994-G-C
• rs7309123
• NM_197947.3:c.612-1404C>G

Variant summary

Our verdict is Benign. The variant received -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]

ENSG00000299754 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CLEC7A	NM_197947.3	c.612-1404C>G		intron_variant	Intron 5 of 5	ENST00000304084.13	NP_922938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC7A	ENST00000304084.13	c.612-1404C>G		intron_variant	Intron 5 of 5	1	NM_197947.3	ENSP00000302569.8

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

African (AFR) AF: 0.142 AC: 5883 AN: 41462

American (AMR) AF: 0.480 AC: 7341 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3466

East Asian (EAS) AF: 0.188 AC: 973 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5668 AN: 10494

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38972 AN: 67936

Other (OTH) AF: 0.483 AC: 1017 AN: 2104

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
PhyloP100		2.1
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

Publications

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Other links and lift over

dbSNP: rs7309123; hg19: chr12-10272593;