16-11117696-A-G

Variant names:

• chr16-11117696-A-G
• rs2080272
• NM_015226.3:c.2117-2919A>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.2117-2919A>G 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 152,064 control chromosomes in the GnomAD database, including 38,450 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 (38450 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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.2117-2919A>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-2919A>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-2919A>G		intron	N/A	NP_001230332.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-2919A>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-2919A>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000904405.1		c.2111-2919A>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106226 AN: 151946 Hom.: 38403 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.699 AC: 106325 AN: 152064 Hom.: 38450 Cov.: 32 AF XY: 0.693 AC XY: 51493 AN XY: 74326

African (AFR) AF: 0.878 AC: 36470 AN: 41520

American (AMR) AF: 0.567 AC: 8651 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2189 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2457 AN: 5152

South Asian (SAS) AF: 0.784 AC: 3781 AN: 4824

European-Finnish (FIN) AF: 0.572 AC: 6036 AN: 10544

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44465 AN: 67974

Other (OTH) AF: 0.691 AC: 1460 AN: 2112

Alfa AF: 0.655 Hom.: 18200

Bravo AF: 0.702

Asia WGS AF: 0.637 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.52
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: rs2080272; hg19: chr16-11211553;