NM_015226.3:c.2642-10916G>A

Variant names:

• chr16-11155472-G-A
• rs6498169
• NM_015226.3:c.2642-10916G>A

Variant summary

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

The NM_015226.3(CLEC16A):​c.2642-10916G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,148 control chromosomes in the GnomAD database, including 33,480 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 0.66 (33480 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 63 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)

ENSG00000287121 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.736 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.2642-10916G>A		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2636-10916G>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.2642-10916G>A		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000904405.1		c.2636-10916G>A		intron	N/A	ENSP00000574464.1
	CLEC16A	ENST00000923410.1		c.2588-10916G>A		intron	N/A	ENSP00000593469.1

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100051 AN: 152028 Hom.: 33468 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.658 AC: 100108 AN: 152148 Hom.: 33480 Cov.: 33 AF XY: 0.653 AC XY: 48580 AN XY: 74364

African (AFR) AF: 0.741 AC: 30766 AN: 41530

American (AMR) AF: 0.559 AC: 8539 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2202 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2297 AN: 5158

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4824

European-Finnish (FIN) AF: 0.572 AC: 6051 AN: 10570

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44387 AN: 67990

Other (OTH) AF: 0.658 AC: 1392 AN: 2116

Alfa AF: 0.642 Hom.: 63329

Bravo AF: 0.656

Asia WGS AF: 0.598 AC: 2082 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	0.35
DANN	Benign	0.78
PhyloP100		-0.17
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: rs6498169; hg19: chr16-11249329;