rs62026376

chr16-11134855-C-T

Variant summary

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

The NM_015226.3(CLEC16A):c.2641+8709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,180 control chromosomes in the GnomAD database, including 3,348 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 0.19 (3348 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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]

LOC105371081 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2641+8709C>T		intron_variant		ENST00000409790.6
LOC105371081	XR_001752081.2	n.88+108G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2641+8709C>T		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28290 AN: 152062 Hom.: 3350 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.186 AC: 28272 AN: 152180 Hom.: 3348 Cov.: 32 AF XY: 0.185 AC XY: 13742 AN XY: 74398

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.215

Alfa AF: 0.204 Hom.: 474

Bravo AF: 0.173

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.0
Dann	Benign	0.71

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: rs62026376; hg19: chr16-11228712;