12-8128312-C-T

Position:

• chr12-8128312-C-T

Variant summary

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

The NM_016184.4(CLEC4A):​c.200-952C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,786 control chromosomes in the GnomAD database, including 28,626 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 0.60 (28626 hom., cov: 30)
• Consequence: CLEC4A NM_016184.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

Genes affected

CLEC4A (HGNC:13257): (C-type lectin domain family 4 member A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. 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]

ENSG00000284697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC4A	NM_016184.4	c.200-952C>T		intron_variant		ENST00000229332.12	NP_057268.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC4A	ENST00000229332.12	c.200-952C>T		intron_variant		1	NM_016184.4	ENSP00000229332.5

Frequencies

GnomAD3 genomes AF: 0.602 AC: 91376 AN: 151670 Hom.: 28613 Cov.: 30

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.602 AC: 91435 AN: 151786 Hom.: 28626 Cov.: 30 AF XY: 0.596 AC XY: 44204 AN XY: 74148

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.635

Alfa AF: 0.677 Hom.: 46100

Bravo AF: 0.593

Asia WGS AF: 0.437 AC: 1521 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	0.91
DANN	Benign	0.51

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: rs2377422; hg19: chr12-8280908;