rs17684919

Variant names:

• chr16-11140988-C-T
• rs17684919
• NM_015226.3:c.2641+14842C>T

Variant summary

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

The NM_015226.3(CLEC16A):​c.2641+14842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,284 control chromosomes in the GnomAD database, including 497 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 0.074 (497 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2641+14842C>T		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.2641+14842C>T		intron_variant	Intron 22 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11344 AN: 152166 Hom.: 498 Cov.: 33

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0745 AC: 11339 AN: 152284 Hom.: 497 Cov.: 33 AF XY: 0.0744 AC XY: 5538 AN XY: 74452

African (AFR) AF: 0.0344 AC: 1431 AN: 41570

American (AMR) AF: 0.0858 AC: 1313 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3472

East Asian (EAS) AF: 0.111 AC: 574 AN: 5178

South Asian (SAS) AF: 0.0406 AC: 196 AN: 4826

European-Finnish (FIN) AF: 0.0867 AC: 920 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0941 AC: 6400 AN: 68014

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0796 Hom.: 156

Bravo AF: 0.0737

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.47
PhyloP100		-0.79
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: rs17684919; hg19: chr16-11234845;