16-11011577-C-G

Variant names:

• chr16-11011577-C-G
• rs7186166
• NM_015226.3:c.1303+8272C>G

Variant summary

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

The NM_015226.3(CLEC16A):​c.1303+8272C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,814 control chromosomes in the GnomAD database, including 7,745 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 0.29 (7745 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

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 (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1303+8272C>G		intron_variant	Intron 11 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1303+8272C>G		intron_variant	Intron 11 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1249+8320C>G		intron_variant	Intron 10 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1297+8272C>G		intron_variant	Intron 10 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.778+8272C>G		intron_variant	Intron 6 of 7	3

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44289 AN: 151696 Hom.: 7728 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.292 AC: 44350 AN: 151814 Hom.: 7745 Cov.: 31 AF XY: 0.289 AC XY: 21454 AN XY: 74200

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.282

Alfa AF: 0.127 Hom.: 202

Bravo AF: 0.304

Asia WGS AF: 0.230 AC: 799 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	7.0
DANN	Benign	0.77

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: rs7186166; hg19: chr16-11105434;