16-11069469-C-G

Variant names:

• chr16-11069469-C-G
• rs7195452
• NM_015226.3:c.2116+8447C>G

Variant summary

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

The NM_015226.3(CLEC16A):​c.2116+8447C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,806 control chromosomes in the GnomAD database, including 1,199 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 0.12 (1199 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 2 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)

ENSG00000262020 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 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.2116+8447C>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2110+8447C>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2062+8447C>G		intron	N/A	NP_001230332.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2116+8447C>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2062+8447C>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000904405.1		c.2110+8447C>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18884 AN: 151688 Hom.: 1192 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.125 AC: 18917 AN: 151806 Hom.: 1199 Cov.: 31 AF XY: 0.124 AC XY: 9166 AN XY: 74176

African (AFR) AF: 0.146 AC: 6046 AN: 41374

American (AMR) AF: 0.106 AC: 1616 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.120 AC: 618 AN: 5164

South Asian (SAS) AF: 0.126 AC: 602 AN: 4790

European-Finnish (FIN) AF: 0.131 AC: 1377 AN: 10520

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8005 AN: 67948

Other (OTH) AF: 0.127 AC: 266 AN: 2100

Alfa AF: 0.115 Hom.: 132

Bravo AF: 0.125

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7195452; hg19: chr16-11163326;