chr16-10947512-C-G

Variant names:

• chr16-10947512-C-G
• rs8051196
• NM_015226.3:c.80+2715C>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.80+2715C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,298 control chromosomes in the GnomAD database, including 63,402 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 0.91 (63402 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.946 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+2715C>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.80+2715C>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.80+2715C>G		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+2715C>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.80+2715C>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.80+2715C>G		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138584 AN: 152180 Hom.: 63360 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.911 AC: 138683 AN: 152298 Hom.: 63402 Cov.: 33 AF XY: 0.911 AC XY: 67887 AN XY: 74488

African (AFR) AF: 0.816 AC: 33878 AN: 41524

American (AMR) AF: 0.920 AC: 14080 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3294 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4615 AN: 5184

South Asian (SAS) AF: 0.957 AC: 4622 AN: 4830

European-Finnish (FIN) AF: 0.981 AC: 10421 AN: 10626

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64763 AN: 68042

Other (OTH) AF: 0.911 AC: 1926 AN: 2114

Alfa AF: 0.927 Hom.: 3651

Bravo AF: 0.901

Asia WGS AF: 0.899 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-3.7
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: rs8051196; hg19: chr16-11041369;