16-11114037-T-C

Position:

• chr16-11114037-T-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-6578T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,054 control chromosomes in the GnomAD database, including 7,877 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 0.32 (7877 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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 = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2117-6578T>C		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-6578T>C		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48770 AN: 151936 Hom.: 7844 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.321 AC: 48853 AN: 152054 Hom.: 7877 Cov.: 32 AF XY: 0.320 AC XY: 23746 AN XY: 74308

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.328

Alfa AF: 0.317 Hom.: 5235

Bravo AF: 0.317

Asia WGS AF: 0.337 AC: 1171 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	2.7
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: rs9746695; hg19: chr16-11207894;