16-10948382-G-A

Position:

• chr16-10948382-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.80+3585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,036 control chromosomes in the GnomAD database, including 9,232 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 0.34 (9232 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.80+3585G>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.80+3585G>A		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.80+3585G>A		intron_variant		1
CLEC16A	ENST00000703130.1	c.80+3585G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51788 AN: 151918 Hom.: 9216 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.341 AC: 51848 AN: 152036 Hom.: 9232 Cov.: 32 AF XY: 0.337 AC XY: 25032 AN XY: 74278

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.315

Alfa AF: 0.326 Hom.: 10861

Bravo AF: 0.343

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.47

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: rs8055533; hg19: chr16-11042239;