rs12928537

Positions:

• chr16-11097543-G-A

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-23072G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,036 control chromosomes in the GnomAD database, including 8,499 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 0.33 (8499 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2117-23072G>A		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-23072G>A		intron_variant		5	NM_015226.3	ENSP00000387122	A1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50585 AN: 151918 Hom.: 8469 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.333 AC: 50667 AN: 152036 Hom.: 8499 Cov.: 32 AF XY: 0.332 AC XY: 24661 AN XY: 74310

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.345

Alfa AF: 0.310 Hom.: 1428

Bravo AF: 0.328

Asia WGS AF: 0.332 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.60

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: rs12928537; hg19: chr16-11191400;