chr16-78058281-T-G

Variant names:

• chr16-78058281-T-G
• rs1922604
• ENST00000563114.1:n.41+1133A>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+1133A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,706 control chromosomes in the GnomAD database, including 35,448 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 (35448 hom., cov: 34)
• Consequence: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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+1133A>C		intron	N/A
	CLEC3A	ENST00000567430.2	TSL:1	n.*181+6132T>G		intron	N/A	ENSP00000457211.2
	ENSG00000261540	ENST00000767192.1		n.186+1604A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102652 AN: 151588 Hom.: 35403 Cov.: 34

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.677 AC: 102752 AN: 151706 Hom.: 35448 Cov.: 34 AF XY: 0.677 AC XY: 50187 AN XY: 74122

African (AFR) AF: 0.800 AC: 33124 AN: 41384

American (AMR) AF: 0.578 AC: 8828 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2374 AN: 3462

East Asian (EAS) AF: 0.648 AC: 3329 AN: 5140

South Asian (SAS) AF: 0.543 AC: 2618 AN: 4820

European-Finnish (FIN) AF: 0.714 AC: 7495 AN: 10490

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

European-Non Finnish (NFE) AF: 0.634 AC: 43032 AN: 67832

Other (OTH) AF: 0.618 AC: 1301 AN: 2104

Alfa AF: 0.645 Hom.: 73998

Bravo AF: 0.675

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.38
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs1922604; hg19: chr16-78092178;