rs12932833

Positions:

• chr16-11084213-C-G

Variant summary

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

The NM_015226.3(CLEC16A):​c.2116+23191C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,996 control chromosomes in the GnomAD database, including 2,315 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 0.16 (2315 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2116+23191C>G		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+23191C>G		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24982 AN: 151878 Hom.: 2311 Cov.: 31

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 25003 AN: 151996 Hom.: 2315 Cov.: 31 AF XY: 0.164 AC XY: 12209 AN XY: 74304

Gnomad4 AFR AF: 0.0804

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.0653

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.179

Alfa AF: 0.181 Hom.: 343

Bravo AF: 0.155

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.53

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: rs12932833; hg19: chr16-11178070;