rs887864

chr16-11065028-G-Achr16-11065028-G-Cchr16-11065028-G-T

Variant summary

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

The NM_015226.3(CLEC16A):c.2116+4006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,010 control chromosomes in the GnomAD database, including 31,459 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 0.64 (31459 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2116+4006G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+4006G>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97446 AN: 151892 Hom.: 31441 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.641 AC: 97505 AN: 152010 Hom.: 31459 Cov.: 31 AF XY: 0.645 AC XY: 47945 AN XY: 74326

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.627

Alfa AF: 0.638 Hom.: 54630

Bravo AF: 0.645

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.11
Dann	Benign	0.29

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: rs887864; hg19: chr16-11158885;