rs13330041

Variant names:

• chr16-10994951-G-A
• rs13330041
• NM_015226.3:c.1072-8123G>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.1072-8123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,114 control chromosomes in the GnomAD database, including 5,058 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 0.25 (5058 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 14 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.1072-8123G>A		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.1066-8123G>A		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.1066-8123G>A		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.1072-8123G>A		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.1066-8123G>A		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.1066-8123G>A		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37329 AN: 151996 Hom.: 5049 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.246 AC: 37363 AN: 152114 Hom.: 5058 Cov.: 32 AF XY: 0.243 AC XY: 18067 AN XY: 74394

African (AFR) AF: 0.351 AC: 14552 AN: 41452

American (AMR) AF: 0.192 AC: 2938 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3472

East Asian (EAS) AF: 0.0974 AC: 504 AN: 5176

South Asian (SAS) AF: 0.205 AC: 990 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1928 AN: 10598

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14647 AN: 67990

Other (OTH) AF: 0.250 AC: 527 AN: 2110

Alfa AF: 0.219 Hom.: 2979

Bravo AF: 0.249

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.40
PhyloP100		-0.43
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: rs13330041; hg19: chr16-11088808;