NM_015226.3:c.2116+14804T>G

Variant names:

• chr16-11075826-T-G
• rs725613
• NM_015226.3:c.2116+14804T>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.2116+14804T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,846 control chromosomes in the GnomAD database, including 14,357 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 0.42 (14357 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 59 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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.2116+14804T>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2110+14804T>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2062+14804T>G		intron	N/A	NP_001230332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2116+14804T>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2062+14804T>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2110+14804T>G		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63631 AN: 151726 Hom.: 14314 Cov.: 30

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.420 AC: 63729 AN: 151846 Hom.: 14357 Cov.: 30 AF XY: 0.416 AC XY: 30884 AN XY: 74212

African (AFR) AF: 0.591 AC: 24428 AN: 41356

American (AMR) AF: 0.329 AC: 5020 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3466

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5156

South Asian (SAS) AF: 0.406 AC: 1950 AN: 4804

European-Finnish (FIN) AF: 0.359 AC: 3789 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24618 AN: 67928

Other (OTH) AF: 0.418 AC: 884 AN: 2116

Alfa AF: 0.383 Hom.: 36312

Bravo AF: 0.422

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.10
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: rs725613; hg19: chr16-11169683;