chr16-10946769-A-T

Variant names:

• chr16-10946769-A-T
• rs12922318
• NM_015226.3:c.80+1972A>T

Variant summary

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

The NM_015226.3(CLEC16A):​c.80+1972A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,098 control chromosomes in the GnomAD database, including 39,909 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 0.71 (39909 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.799 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.80+1972A>T		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.80+1972A>T		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.80+1972A>T		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.80+1972A>T		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.80+1972A>T		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000904405.1		c.80+1972A>T		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107442 AN: 151980 Hom.: 39907 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.707 AC: 107482 AN: 152098 Hom.: 39909 Cov.: 32 AF XY: 0.712 AC XY: 52920 AN XY: 74358

African (AFR) AF: 0.456 AC: 18875 AN: 41404

American (AMR) AF: 0.772 AC: 11804 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2741 AN: 3468

East Asian (EAS) AF: 0.776 AC: 4016 AN: 5176

South Asian (SAS) AF: 0.813 AC: 3927 AN: 4828

European-Finnish (FIN) AF: 0.842 AC: 8932 AN: 10608

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54746 AN: 68004

Other (OTH) AF: 0.721 AC: 1526 AN: 2116

Alfa AF: 0.739 Hom.: 5326

Bravo AF: 0.689

Asia WGS AF: 0.761 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.76
PhyloP100		0.070
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: rs12922318; hg19: chr16-11040626;