chr16-11163244-A-G

Variant names:

• chr16-11163244-A-G
• rs27908
• NM_015226.3:c.2642-3144A>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.2642-3144A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,128 control chromosomes in the GnomAD database, including 36,647 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 0.69 (36647 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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.2642-3144A>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2636-3144A>G		intron	N/A	NP_001397834.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2642-3144A>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000703130.1		c.2636-3144A>G		intron	N/A	ENSP00000515187.1
	CLEC16A	ENST00000261657.5	TSL:4	c.215-3144A>G		intron	N/A	ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104157 AN: 152010 Hom.: 36613 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.685 AC: 104238 AN: 152128 Hom.: 36647 Cov.: 33 AF XY: 0.679 AC XY: 50488 AN XY: 74346

African (AFR) AF: 0.821 AC: 34092 AN: 41520

American (AMR) AF: 0.572 AC: 8746 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2262 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2324 AN: 5158

South Asian (SAS) AF: 0.761 AC: 3668 AN: 4822

European-Finnish (FIN) AF: 0.573 AC: 6055 AN: 10574

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44820 AN: 67984

Other (OTH) AF: 0.681 AC: 1436 AN: 2108

Alfa AF: 0.663 Hom.: 90278

Bravo AF: 0.686

Asia WGS AF: 0.607 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		1.2
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: rs27908; hg19: chr16-11257101;