rs7200786

chr16-11083944-A-Gchr16-11083944-A-T

Variant summary

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

The NM_015226.3(CLEC16A):c.2116+22922A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,930 control chromosomes in the GnomAD database, including 26,535 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 0.58 (26535 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2116+22922A>G		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2116+22922A>G		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88276 AN: 151812 Hom.: 26483 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.582 AC: 88386 AN: 151930 Hom.: 26535 Cov.: 32 AF XY: 0.576 AC XY: 42760 AN XY: 74262

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.566

Alfa AF: 0.543 Hom.: 11647

Bravo AF: 0.583

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.3
Dann	Benign	0.72

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: rs7200786; hg19: chr16-11177801;