rs42369

Variant names:

• chr16-11170755-G-A
• rs42369
• NM_015226.3:c.2806+4203G>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.2806+4203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,168 control chromosomes in the GnomAD database, including 35,405 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 0.68 (35405 hom., cov: 34)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2806+4203G>A		intron_variant	Intron 23 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2806+4203G>A		intron_variant	Intron 23 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000703130.1	c.2800+4203G>A		intron_variant	Intron 22 of 22			ENSP00000515187.1
CLEC16A	ENST00000261657.5	c.380-3399G>A		intron_variant	Intron 3 of 4	4		ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103240 AN: 152050 Hom.: 35365 Cov.: 34

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.679 AC: 103331 AN: 152168 Hom.: 35405 Cov.: 34 AF XY: 0.681 AC XY: 50693 AN XY: 74404

African (AFR) AF: 0.725 AC: 30102 AN: 41500

American (AMR) AF: 0.790 AC: 12084 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2249 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3365 AN: 5170

South Asian (SAS) AF: 0.754 AC: 3636 AN: 4820

European-Finnish (FIN) AF: 0.581 AC: 6154 AN: 10590

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43490 AN: 68002

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.653 Hom.: 146863

Bravo AF: 0.695

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		0.0030
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: rs42369; hg19: chr16-11264612;