NM_015226.3:c.1866+1521T>C

Variant names:

• chr16-11048863-T-C
• rs3901386
• NM_015226.3:c.1866+1521T>C

Variant summary

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

The NM_015226.3(CLEC16A):​c.1866+1521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,614 control chromosomes in the GnomAD database, including 19,303 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 (19303 hom., cov: 29)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 25 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1866+1521T>C		intron_variant	Intron 17 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1866+1521T>C		intron_variant	Intron 17 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74189 AN: 151496 Hom.: 19250 Cov.: 29

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.490 AC: 74297 AN: 151614 Hom.: 19303 Cov.: 29 AF XY: 0.485 AC XY: 35944 AN XY: 74060

African (AFR) AF: 0.675 AC: 27888 AN: 41294

American (AMR) AF: 0.403 AC: 6144 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1746 AN: 3466

East Asian (EAS) AF: 0.339 AC: 1740 AN: 5134

South Asian (SAS) AF: 0.435 AC: 2069 AN: 4756

European-Finnish (FIN) AF: 0.400 AC: 4217 AN: 10538

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28936 AN: 67884

Other (OTH) AF: 0.493 AC: 1036 AN: 2102

Alfa AF: 0.433 Hom.: 10601

Bravo AF: 0.496

Asia WGS AF: 0.452 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.99
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: rs3901386; hg19: chr16-11142720;