rs12931878

Positions:

• chr16-10948337-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.80+3540A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,236 control chromosomes in the GnomAD database, including 1,992 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 0.14 (1992 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

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 = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.80+3540A>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.80+3540A>G		intron_variant		5	NM_015226.3	ENSP00000387122	A1
CLEC16A	ENST00000409552.4	c.80+3540A>G		intron_variant		1		ENSP00000386495
CLEC16A	ENST00000703130.1	c.80+3540A>G		intron_variant				ENSP00000515187	P4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22048 AN: 152116 Hom.: 1991 Cov.: 33

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.145 AC: 22046 AN: 152236 Hom.: 1992 Cov.: 33 AF XY: 0.144 AC XY: 10713 AN XY: 74442

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.181

Alfa AF: 0.173 Hom.: 1184

Bravo AF: 0.137

Asia WGS AF: 0.184 AC: 641 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	6.4
DANN	Benign	0.67

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: rs12931878; hg19: chr16-11042194;