rs2867880

chr16-11138000-G-Achr16-11138000-G-Cchr16-11138000-G-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+11854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,058 control chromosomes in the GnomAD database, including 9,048 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 0.34 (9048 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2641+11854G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2641+11854G>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52102 AN: 151940 Hom.: 9029 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.343 AC: 52160 AN: 152058 Hom.: 9048 Cov.: 32 AF XY: 0.342 AC XY: 25402 AN XY: 74324

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.358

Alfa AF: 0.252 Hom.: 1063

Bravo AF: 0.338

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.24
Dann	Benign	0.50

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: rs2867880; hg19: chr16-11231857; COSMIC: COSV55488486; COSMIC: COSV55488486;