16-10949556-C-T

Variant names:

• chr16-10949556-C-T
• rs7205474
• NM_015226.3:c.80+4759C>T

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+4759C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,716 control chromosomes in the GnomAD database, including 4,640 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 0.22 (4640 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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.80+4759C>T		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.80+4759C>T		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.80+4759C>T		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.80+4759C>T		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.80+4759C>T		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000904405.1		c.80+4759C>T		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33681 AN: 151598 Hom.: 4621 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.222 AC: 33745 AN: 151716 Hom.: 4640 Cov.: 31 AF XY: 0.219 AC XY: 16230 AN XY: 74134

African (AFR) AF: 0.395 AC: 16311 AN: 41300

American (AMR) AF: 0.152 AC: 2311 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3466

East Asian (EAS) AF: 0.119 AC: 606 AN: 5112

South Asian (SAS) AF: 0.152 AC: 731 AN: 4794

European-Finnish (FIN) AF: 0.178 AC: 1884 AN: 10566

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10728 AN: 67924

Other (OTH) AF: 0.208 AC: 439 AN: 2108

Alfa AF: 0.186 Hom.: 659

Bravo AF: 0.227

Asia WGS AF: 0.147 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.58
PhyloP100		-0.82
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: rs7205474; hg19: chr16-11043413;