rs794426

chr16-11149001-C-Achr16-11149001-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015226.3(CLEC16A):c.2642-17387C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,120 control chromosomes in the GnomAD database, including 38,507 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 0.70 (38507 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2642-17387C>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2642-17387C>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106172 AN: 152002 Hom.: 38459 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.699 AC: 106271 AN: 152120 Hom.: 38507 Cov.: 33 AF XY: 0.692 AC XY: 51439 AN XY: 74348

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.686

Alfa AF: 0.668 Hom.: 30644

Bravo AF: 0.703

Asia WGS AF: 0.617 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	14
Dann	Benign	0.79

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: rs794426; hg19: chr16-11242858;