rs62026376

Variant names:

• chr16-11134855-C-T
• rs62026376
• NM_015226.3:c.2641+8709C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

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]

CLEC16A Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

LOC105371081 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2641+8709C>T		intron_variant	Intron 22 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2641+8709C>T		intron_variant	Intron 22 of 23	5	NM_015226.3	ENSP00000387122.1

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

African (AFR) AF: 0.0457 AC: 1901 AN: 41560

American (AMR) AF: 0.189 AC: 2885 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3468

East Asian (EAS) AF: 0.0732 AC: 379 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2372 AN: 10578

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17498 AN: 67966

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.215 Hom.: 6499

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
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs62026376; hg19: chr16-11228712;