rs2003400

Variant names:

• chr16-11125464-G-A
• rs2003400
• NM_015226.3:c.2474-515G>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.2474-515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,012 control chromosomes in the GnomAD database, including 10,107 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 0.35 (10107 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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.2474-515G>A		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2468-515G>A		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.2420-515G>A		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2474-515G>A		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.2420-515G>A		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.2468-515G>A		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52852 AN: 151896 Hom.: 10099 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.348 AC: 52890 AN: 152012 Hom.: 10107 Cov.: 32 AF XY: 0.343 AC XY: 25482 AN XY: 74320

African (AFR) AF: 0.520 AC: 21549 AN: 41426

American (AMR) AF: 0.273 AC: 4169 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1173 AN: 5162

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4810

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10584

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20135 AN: 67966

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.305 Hom.: 9696

Bravo AF: 0.356

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.2
DANN	Benign	0.52
PhyloP100		1.3
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: rs2003400; hg19: chr16-11219321;