16-11109708-G-C

Variant names:

• chr16-11109708-G-C
• rs9926078
• NM_015226.3:c.2117-10907G>C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-10907G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,050 control chromosomes in the GnomAD database, including 15,482 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 0.45 (15482 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 8 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 = 0.514 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.2117-10907G>C		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-10907G>C		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-10907G>C		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.2117-10907G>C		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-10907G>C		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2111-10907G>C		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68017 AN: 151930 Hom.: 15452 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.448 AC: 68097 AN: 152050 Hom.: 15482 Cov.: 32 AF XY: 0.444 AC XY: 32995 AN XY: 74302

African (AFR) AF: 0.520 AC: 21568 AN: 41462

American (AMR) AF: 0.382 AC: 5840 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1706 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5156

South Asian (SAS) AF: 0.437 AC: 2102 AN: 4812

European-Finnish (FIN) AF: 0.401 AC: 4245 AN: 10586

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29351 AN: 67964

Other (OTH) AF: 0.462 AC: 977 AN: 2114

Alfa AF: 0.285 Hom.: 666

Bravo AF: 0.449

Asia WGS AF: 0.437 AC: 1517 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	2.2
DANN	Benign	0.47
PhyloP100		-0.48
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: rs9926078; hg19: chr16-11203565;