rs2222896

Positions:

• chr16-78058601-A-G

Variant summary

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

The ENST00000567430.2(CLEC3A):​c.*181+6452A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,080 control chromosomes in the GnomAD database, including 35,608 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 0.68 (35608 hom., cov: 32)
• Consequence: CLEC3A ENST00000567430.2 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

CLEC3A (HGNC:2052): (C-type lectin domain family 3 member A) Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984897	XR_001752267.2	n.354-5112A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC3A	ENST00000567430.2	c.*181+6452A>G		intron_variant, NMD_transcript_variant		1
	ENST00000563114.1	n.41+813T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102975 AN: 151962 Hom.: 35563 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.678 AC: 103075 AN: 152080 Hom.: 35608 Cov.: 32 AF XY: 0.678 AC XY: 50357 AN XY: 74300

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.620

Alfa AF: 0.644 Hom.: 12506

Bravo AF: 0.674

Asia WGS AF: 0.559 AC: 1947 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	4.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2222896; hg19: chr16-78092498;