rs12935657

chr16-11125184-G-Achr16-11125184-G-T

Variant summary

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

The NM_015226.3(CLEC16A):c.2474-795G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,138 control chromosomes in the GnomAD database, including 3,265 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 0.19 (3265 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2474-795G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2474-795G>A		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28168 AN: 152020 Hom.: 3266 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.185 AC: 28155 AN: 152138 Hom.: 3265 Cov.: 32 AF XY: 0.184 AC XY: 13678 AN XY: 74380

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0620

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.215

Alfa AF: 0.143 Hom.: 461

Bravo AF: 0.173

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.0090
Dann	Benign	0.93

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: rs12935657; hg19: chr16-11219041;