rs12932833

Variant names:

• chr16-11084213-C-G
• rs12932833
• NM_015226.3:c.2116+23191C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-11084213-C-G
• chr16-11084213-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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.2116+23191C>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2110+23191C>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2062+23191C>G		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.2116+23191C>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2062+23191C>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2110+23191C>G		intron	N/A	ENSP00000515187.1

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

African (AFR) AF: 0.0804 AC: 3333 AN: 41474

American (AMR) AF: 0.156 AC: 2387 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.0653 AC: 338 AN: 5174

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4804

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10564

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14075 AN: 67932

Other (OTH) AF: 0.179 AC: 377 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.53
PhyloP100		-0.23
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: rs12932833; hg19: chr16-11178070;