rs27838

Variant names:

• chr16-11159626-G-A
• rs27838
• NM_015226.3:c.2642-6762G>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.2642-6762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,208 control chromosomes in the GnomAD database, including 38,843 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 0.70 (38843 hom., cov: 34)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90
• Publications: 7 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)

ENSG00000287121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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.2642-6762G>A		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2636-6762G>A		intron	N/A	NP_001397834.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2642-6762G>A		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000703130.1		c.2636-6762G>A		intron	N/A	ENSP00000515187.1
	CLEC16A	ENST00000261657.5	TSL:4	c.215-6762G>A		intron	N/A	ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106802 AN: 152090 Hom.: 38795 Cov.: 34

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.702 AC: 106901 AN: 152208 Hom.: 38843 Cov.: 34 AF XY: 0.696 AC XY: 51762 AN XY: 74402

African (AFR) AF: 0.876 AC: 36426 AN: 41560

American (AMR) AF: 0.577 AC: 8818 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2341 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2328 AN: 5170

South Asian (SAS) AF: 0.764 AC: 3687 AN: 4826

European-Finnish (FIN) AF: 0.572 AC: 6048 AN: 10582

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44934 AN: 68000

Other (OTH) AF: 0.695 AC: 1468 AN: 2112

Alfa AF: 0.670 Hom.: 16050

Bravo AF: 0.706

Asia WGS AF: 0.615 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0090
DANN	Benign	0.41
PhyloP100		-2.9
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: rs27838; hg19: chr16-11253483;