16-78034329-A-G

Position:

• chr16-78034329-A-G

Variant summary

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

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: intergenic_region
• 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/exons	MANE	Protein	UniProt
		n.78034329A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261540	ENST00000563114.1	n.42-19200T>C		intron_variant		1
CLEC3A	ENST00000567430.2	n.115+11588A>G		intron_variant		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;