chr16-11067109-A-C

Position:

• chr16-11067109-A-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2116+6087A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 149,972 control chromosomes in the GnomAD database, including 44,371 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 0.77 (44371 hom., cov: 25)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2116+6087A>C		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+6087A>C		intron_variant		5	NM_015226.3	ENSP00000387122	A1
	ENST00000572828.1	n.353-356T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 115168 AN: 149870 Hom.: 44339 Cov.: 25

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.768 AC: 115246 AN: 149972 Hom.: 44371 Cov.: 25 AF XY: 0.772 AC XY: 56402 AN XY: 73038

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.761

Alfa AF: 0.769 Hom.: 5604

Bravo AF: 0.772

Asia WGS AF: 0.824 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.70

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: rs8062923; hg19: chr16-11160966;