NM_015226.3:c.1072-2513G>C

Variant names:

• chr16-11000561-G-C
• rs13337334
• NM_015226.3:c.1072-2513G>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.1072-2513G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,964 control chromosomes in the GnomAD database, including 4,946 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 0.25 (4946 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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.1072-2513G>C		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.1066-2513G>C		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.1066-2513G>C		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.1072-2513G>C		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.1066-2513G>C		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.1066-2513G>C		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38064 AN: 151846 Hom.: 4944 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.251 AC: 38079 AN: 151964 Hom.: 4946 Cov.: 32 AF XY: 0.249 AC XY: 18476 AN XY: 74260

African (AFR) AF: 0.191 AC: 7932 AN: 41446

American (AMR) AF: 0.244 AC: 3719 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5172

South Asian (SAS) AF: 0.248 AC: 1197 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2462 AN: 10540

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19502 AN: 67932

Other (OTH) AF: 0.279 AC: 588 AN: 2108

Alfa AF: 0.144 Hom.: 294

Bravo AF: 0.247

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.012
DANN	Benign	0.39
PhyloP100		-2.2
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: rs13337334; hg19: chr16-11094418;