chr16-11075826-T-G

Position:

• chr16-11075826-T-G

Variant summary

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

The NM_015226.3(CLEC16A):​c.2116+14804T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,846 control chromosomes in the GnomAD database, including 14,357 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 0.42 (14357 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2116+14804T>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.2116+14804T>G		intron_variant		5	NM_015226.3	ENSP00000387122	A1

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63631 AN: 151726 Hom.: 14314 Cov.: 30

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.420 AC: 63729 AN: 151846 Hom.: 14357 Cov.: 30 AF XY: 0.416 AC XY: 30884 AN XY: 74212

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.418

Alfa AF: 0.372 Hom.: 21990

Bravo AF: 0.422

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.56

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: rs725613; hg19: chr16-11169683;