rs9941107

Variant names:

• chr16-11102184-G-A
• rs9941107
• NM_015226.3:c.2117-18431G>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.2117-18431G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,958 control chromosomes in the GnomAD database, including 15,546 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 (15546 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 13 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 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.2117-18431G>A		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-18431G>A		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-18431G>A		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.2117-18431G>A		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-18431G>A		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2111-18431G>A		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68138 AN: 151840 Hom.: 15512 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.449 AC: 68228 AN: 151958 Hom.: 15546 Cov.: 32 AF XY: 0.445 AC XY: 33030 AN XY: 74268

African (AFR) AF: 0.527 AC: 21807 AN: 41404

American (AMR) AF: 0.384 AC: 5854 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1700 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1744 AN: 5176

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4814

European-Finnish (FIN) AF: 0.398 AC: 4201 AN: 10548

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29330 AN: 67970

Other (OTH) AF: 0.466 AC: 984 AN: 2110

Alfa AF: 0.421 Hom.: 3609

Bravo AF: 0.450

Asia WGS AF: 0.433 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.45
DANN	Benign	0.52
PhyloP100		-0.21
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: rs9941107; hg19: chr16-11196041;