rs9923856

Variant names:

• chr16-11116558-T-C
• rs9923856
• NM_015226.3:c.2117-4057T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2117-4057T>C		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-4057T>C		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-4057T>C		intron	N/A	NP_001230332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-4057T>C		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-4057T>C		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2111-4057T>C		intron	N/A	ENSP00000515187.1

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

African (AFR) AF: 0.640 AC: 26536 AN: 41432

American (AMR) AF: 0.339 AC: 5180 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3472

East Asian (EAS) AF: 0.190 AC: 982 AN: 5164

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4810

European-Finnish (FIN) AF: 0.263 AC: 2781 AN: 10584

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21769 AN: 67954

Other (OTH) AF: 0.429 AC: 903 AN: 2104

Alfa AF: 0.342 Hom.: 42079

Bravo AF: 0.420

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.21
PhyloP100		-1.3
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: rs9923856; hg19: chr16-11210415; COSMIC: COSV68502199;