NM_015226.3:c.1815+883G>A

Variant names:

• chr16-11044955-G-A
• rs8056098
• NM_015226.3:c.1815+883G>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.1815+883G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 150,192 control chromosomes in the GnomAD database, including 19,088 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 0.49 (19088 hom., cov: 28)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 15 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1815+883G>A		intron_variant	Intron 16 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1815+883G>A		intron_variant	Intron 16 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73217 AN: 150090 Hom.: 19044 Cov.: 28

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.488 AC: 73309 AN: 150192 Hom.: 19088 Cov.: 28 AF XY: 0.483 AC XY: 35306 AN XY: 73086

African (AFR) AF: 0.681 AC: 27943 AN: 41014

American (AMR) AF: 0.402 AC: 6026 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3464

East Asian (EAS) AF: 0.337 AC: 1719 AN: 5106

South Asian (SAS) AF: 0.427 AC: 2033 AN: 4760

European-Finnish (FIN) AF: 0.384 AC: 3798 AN: 9902

Middle Eastern (MID) AF: 0.466 AC: 135 AN: 290

European-Non Finnish (NFE) AF: 0.421 AC: 28512 AN: 67682

Other (OTH) AF: 0.494 AC: 1024 AN: 2074

Alfa AF: 0.407 Hom.: 6177

Bravo AF: 0.494

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.55
DANN	Benign	0.34
PhyloP100		-0.33
Mutation Taster		=21/79	disease causing

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: rs8056098; hg19: chr16-11138812;