rs17684919

chr16-11140988-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2641+14842C>T		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2641+14842C>T		intron_variant		5	NM_015226.3	A1

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

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.0556

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0406

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0830 Hom.: 141

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs17684919; hg19: chr16-11234845;