rs876457

chr16-11049869-G-A

Variant summary

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

The NM_015226.3(CLEC16A):c.1867-1644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 152,268 control chromosomes in the GnomAD database, including 654 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 0.089 (654 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

CLEC16A (HGNC:29013): (C-type lectin domain containing 16A) This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1867-1644G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1867-1644G>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13605 AN: 152150 Hom.: 652 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0434

Gnomad FIN AF: 0.0647

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0894 AC: 13609 AN: 152268 Hom.: 654 Cov.: 33 AF XY: 0.0890 AC XY: 6625 AN XY: 74440

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.0647

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0918

Alfa AF: 0.0768 Hom.: 216

Bravo AF: 0.0938

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.4
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs876457; hg19: chr16-11143726;