rs6498169

Positions:

• chr16-11155472-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.2642-10916G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,148 control chromosomes in the GnomAD database, including 33,480 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 0.66 (33480 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2642-10916G>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.2642-10916G>A		intron_variant		5	NM_015226.3	ENSP00000387122	A1
	ENST00000667071.1	n.427C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100051 AN: 152028 Hom.: 33468 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.658 AC: 100108 AN: 152148 Hom.: 33480 Cov.: 33 AF XY: 0.653 AC XY: 48580 AN XY: 74364

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.658

Alfa AF: 0.641 Hom.: 43724

Bravo AF: 0.656

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.35
DANN	Benign	0.78

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: rs6498169; hg19: chr16-11249329;