ENST00000563114.1:n.42-19200T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563114.1(ENSG00000261540):​n.42-19200T>C 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: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563114.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261540	ENST00000563114.1	TSL:1	n.42-19200T>C		intron	N/A
	CLEC3A	ENST00000567430.2	TSL:1	n.115+11588A>G		intron	N/A	ENSP00000457211.2
	ENSG00000261540	ENST00000767192.1		n.187-17151T>C		intron	N/A

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

African (AFR) AF: 0.216 AC: 8947 AN: 41440

American (AMR) AF: 0.436 AC: 6642 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3464

East Asian (EAS) AF: 0.478 AC: 2436 AN: 5094

South Asian (SAS) AF: 0.464 AC: 2219 AN: 4786

European-Finnish (FIN) AF: 0.291 AC: 3062 AN: 10520

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25485 AN: 67860

Other (OTH) AF: 0.405 AC: 853 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs2881154; hg19: chr16-78068226;