16-10947512-C-G

Variant summary

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

The NM_015226.3(CLEC16A):c.80+2715C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,298 control chromosomes in the GnomAD database, including 63,402 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 0.91 (63402 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.80+2715C>G		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.80+2715C>G		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.80+2715C>G		intron_variant		1
CLEC16A	ENST00000703130.1	c.80+2715C>G		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138584 AN: 152180 Hom.: 63360 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.911 AC: 138683 AN: 152298 Hom.: 63402 Cov.: 33 AF XY: 0.911 AC XY: 67887 AN XY: 74488

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.911

Alfa AF: 0.927 Hom.: 3651

Bravo AF: 0.901

Asia WGS AF: 0.899 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.29
Dann	Benign	0.35

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: rs8051196; hg19: chr16-11041369;