rs9923856

Positions:

• chr16-11116558-T-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-4057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,998 control chromosomes in the GnomAD database, including 14,254 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 0.41 (14254 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2117-4057T>C		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-4057T>C		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61576 AN: 151880 Hom.: 14228 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.406 AC: 61648 AN: 151998 Hom.: 14254 Cov.: 31 AF XY: 0.401 AC XY: 29758 AN XY: 74292

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.429

Alfa AF: 0.327 Hom.: 17354

Bravo AF: 0.420

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.21

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: rs9923856; hg19: chr16-11210415; COSMIC: COSV68502199;