rs17806056

Variant names:

• chr16-11098642-T-A
• rs17806056
• NM_015226.3:c.2117-21973T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2117-21973T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,262 control chromosomes in the GnomAD database, including 2,995 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 0.18 (2995 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 12 publications found

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]

CLEC16A Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2117-21973T>A		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-21973T>A		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-21973T>A		intron	N/A	NP_001230332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-21973T>A		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-21973T>A		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2111-21973T>A		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27423 AN: 152144 Hom.: 2994 Cov.: 33

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.180 AC: 27428 AN: 152262 Hom.: 2995 Cov.: 33 AF XY: 0.179 AC XY: 13342 AN XY: 74450

African (AFR) AF: 0.0631 AC: 2622 AN: 41560

American (AMR) AF: 0.177 AC: 2703 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3468

East Asian (EAS) AF: 0.0672 AC: 349 AN: 5190

South Asian (SAS) AF: 0.237 AC: 1146 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2307 AN: 10602

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16333 AN: 67996

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.202 Hom.: 439

Bravo AF: 0.169

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17806056; hg19: chr16-11192499;