rs3893660

Variant names:

• chr16-11100073-A-G
• rs3893660
• NM_015226.3:c.2117-20542A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2117-20542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,956 control chromosomes in the GnomAD database, including 16,664 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 0.46 (16664 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 17 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2117-20542A>G		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2111-20542A>G		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.2063-20542A>G		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-20542A>G		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-20542A>G		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.2111-20542A>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70372 AN: 151838 Hom.: 16627 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.464 AC: 70460 AN: 151956 Hom.: 16664 Cov.: 32 AF XY: 0.460 AC XY: 34160 AN XY: 74248

African (AFR) AF: 0.561 AC: 23242 AN: 41424

American (AMR) AF: 0.389 AC: 5941 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1800 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1735 AN: 5168

South Asian (SAS) AF: 0.440 AC: 2116 AN: 4814

European-Finnish (FIN) AF: 0.419 AC: 4416 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29682 AN: 67938

Other (OTH) AF: 0.478 AC: 1009 AN: 2112

Alfa AF: 0.434 Hom.: 4242

Bravo AF: 0.465

Asia WGS AF: 0.436 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.94
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3893660;

hg19: chr16-11193930;