rs16958028

Positions:

• chr16-11082811-A-T

Variant summary

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

The NM_015226.3(CLEC16A):​c.2116+21789A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 152,086 control chromosomes in the GnomAD database, including 697 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 0.097 (697 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

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 (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2116+21789A>T		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+21789A>T		intron_variant		5	NM_015226.3	ENSP00000387122	A1

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14697 AN: 151968 Hom.: 697 Cov.: 33

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0968 AC: 14715 AN: 152086 Hom.: 697 Cov.: 33 AF XY: 0.0972 AC XY: 7226 AN XY: 74346

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0946

Alfa AF: 0.0977 Hom.: 96

Bravo AF: 0.0939

Asia WGS AF: 0.121 AC: 420 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	3.0
DANN	Benign	0.44

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: rs16958028; hg19: chr16-11176668;