16-11121178-A-G

Position:

• chr16-11121178-A-G

Variant summary

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

The NM_015226.3(CLEC16A):​c.2268+412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,264 control chromosomes in the GnomAD database, including 2,594 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 0.17 (2594 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2268+412A>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.2268+412A>G		intron_variant		5	NM_015226.3	ENSP00000387122	A1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25443 AN: 152146 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.167 AC: 25443 AN: 152264 Hom.: 2594 Cov.: 32 AF XY: 0.167 AC XY: 12439 AN XY: 74452

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.189

Alfa AF: 0.165 Hom.: 750

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs34306440; hg19: chr16-11215035;