16-10954493-A-G

Position:

• chr16-10954493-A-G

Variant summary

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

The NM_015226.3(CLEC16A):​c.81-3289A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,042 control chromosomes in the GnomAD database, including 29,792 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 0.61 (29792 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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 (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.81-3289A>G		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.81-3289A>G		intron_variant		5	NM_015226.3	ENSP00000387122	A1
CLEC16A	ENST00000409552.4	c.81-3289A>G		intron_variant		1		ENSP00000386495
CLEC16A	ENST00000703130.1	c.81-3289A>G		intron_variant				ENSP00000515187	P4

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92732 AN: 151922 Hom.: 29742 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.611 AC: 92841 AN: 152042 Hom.: 29792 Cov.: 32 AF XY: 0.604 AC XY: 44883 AN XY: 74332

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.603

Alfa AF: 0.564 Hom.: 12494

Bravo AF: 0.612

Asia WGS AF: 0.514 AC: 1787 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	0.47
DANN	Benign	0.72

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: rs1035089; hg19: chr16-11048350;