rs17673553

Variant names:

• chr16-11148049-A-G
• rs17673553
• NM_015226.3:c.2642-18339A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015226.3(CLEC16A):​c.2642-18339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,142 control chromosomes in the GnomAD database, including 3,357 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 0.19 (3357 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 32 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2642-18339A>G		intron_variant	Intron 22 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2642-18339A>G		intron_variant	Intron 22 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28286 AN: 152024 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.186 AC: 28267 AN: 152142 Hom.: 3357 Cov.: 32 AF XY: 0.185 AC XY: 13770 AN XY: 74384

African (AFR) AF: 0.0453 AC: 1879 AN: 41524

American (AMR) AF: 0.189 AC: 2892 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3472

East Asian (EAS) AF: 0.0765 AC: 396 AN: 5178

South Asian (SAS) AF: 0.265 AC: 1274 AN: 4806

European-Finnish (FIN) AF: 0.226 AC: 2388 AN: 10582

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17375 AN: 67974

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.237 Hom.: 7734

Bravo AF: 0.173

Asia WGS AF: 0.172 AC: 596 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	17
DANN	Benign	0.85
PhyloP100		2.0
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: rs17673553; hg19: chr16-11241906;