rs9652582

chr16-11080707-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):c.2116+19685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,098 control chromosomes in the GnomAD database, including 12,691 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 0.39 (12691 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2116+19685G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+19685G>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59370 AN: 151980 Hom.: 12647 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.391 AC: 59472 AN: 152098 Hom.: 12691 Cov.: 32 AF XY: 0.388 AC XY: 28858 AN XY: 74372

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.384

Alfa AF: 0.333 Hom.: 1688

Bravo AF: 0.394

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.27
Dann	Benign	0.58

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: rs9652582; hg19: chr16-11174564;