rs1922604

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984897	XR_001752267.2	n.354-5432T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261540	ENST00000563114.1	n.41+1133A>C		intron_variant	Intron 1 of 1	1
CLEC3A	ENST00000567430.2	n.*181+6132T>G		intron_variant	Intron 2 of 2	1		ENSP00000457211.2
ENSG00000261540	ENST00000767192.1	n.186+1604A>C		intron_variant	Intron 1 of 2

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 v4.3

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;