chr16-11149001-C-A

Variant names:

• chr16-11149001-C-A
• rs794426
• NM_015226.3:c.2642-17387C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015226.3(CLEC16A):​c.2642-17387C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,120 control chromosomes in the GnomAD database, including 38,507 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 0.70 (38507 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 6 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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.2642-17387C>A		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2636-17387C>A		intron	N/A	NP_001397834.1	A0A8V8TR67

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2642-17387C>A		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000904405.1		c.2636-17387C>A		intron	N/A	ENSP00000574464.1
	CLEC16A	ENST00000923410.1		c.2588-17387C>A		intron	N/A	ENSP00000593469.1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106172 AN: 152002 Hom.: 38459 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.699 AC: 106271 AN: 152120 Hom.: 38507 Cov.: 33 AF XY: 0.692 AC XY: 51439 AN XY: 74348

African (AFR) AF: 0.886 AC: 36802 AN: 41536

American (AMR) AF: 0.571 AC: 8715 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2327 AN: 5170

South Asian (SAS) AF: 0.750 AC: 3618 AN: 4824

European-Finnish (FIN) AF: 0.568 AC: 5999 AN: 10564

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44274 AN: 67960

Other (OTH) AF: 0.686 AC: 1450 AN: 2114

Alfa AF: 0.673 Hom.: 40498

Bravo AF: 0.703

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		1.7
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: rs794426; hg19: chr16-11242858;