16-78034329-A-G

Variant names:

• chr16-78034329-A-G
• rs2881154
• ENST00000563114.1:n.42-19200T>C

Variant summary

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

The ENST00000567430.2(CLEC3A):​n.115+11588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,716 control chromosomes in the GnomAD database, including 9,485 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 0.34 (9485 hom., cov: 30)
• Consequence: CLEC3A ENST00000567430.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

ENSG00000261540 (HGNC:):

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]

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 (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261540	ENST00000563114.1	n.42-19200T>C		intron_variant	Intron 1 of 1	1
CLEC3A	ENST00000567430.2	n.115+11588A>G		intron_variant	Intron 1 of 2	1		ENSP00000457211.2

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51395 AN: 151598 Hom.: 9478 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.339 AC: 51408 AN: 151716 Hom.: 9485 Cov.: 30 AF XY: 0.340 AC XY: 25202 AN XY: 74140

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.405

Alfa AF: 0.232 Hom.: 660

Bravo AF: 0.345

Asia WGS AF: 0.420 AC: 1225 AN: 2918

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2881154; hg19: chr16-78068226;