16-78058601-A-G

Variant names:

• chr16-78058601-A-G
• rs2222896
• ENST00000563114.1:n.41+813T>C

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.41+813T>C variant causes a intron 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: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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.41+813T>C		intron	N/A
	CLEC3A	ENST00000567430.2	TSL:1	n.*181+6452A>G		intron	N/A	ENSP00000457211.2
	ENSG00000261540	ENST00000767192.1		n.186+1284T>C		intron	N/A

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

African (AFR) AF: 0.801 AC: 33248 AN: 41498

American (AMR) AF: 0.578 AC: 8839 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3350 AN: 5154

South Asian (SAS) AF: 0.545 AC: 2620 AN: 4810

European-Finnish (FIN) AF: 0.716 AC: 7563 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43106 AN: 67980

Other (OTH) AF: 0.620 AC: 1309 AN: 2110

Alfa AF: 0.646 Hom.: 14421

Bravo AF: 0.674

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2222896; hg19: chr16-78092498;