rs17803698

Variant names:

• chr16-10976432-A-G
• rs17803698
• NM_015226.3:c.729-793A>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.729-793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 151,950 control chromosomes in the GnomAD database, including 1,770 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 0.15 (1770 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 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.729-793A>G		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.723-793A>G		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.723-793A>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.729-793A>G		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.723-793A>G		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.723-793A>G		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22873 AN: 151834 Hom.: 1765 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.151 AC: 22902 AN: 151950 Hom.: 1770 Cov.: 31 AF XY: 0.149 AC XY: 11069 AN XY: 74254

African (AFR) AF: 0.126 AC: 5208 AN: 41432

American (AMR) AF: 0.141 AC: 2154 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3472

East Asian (EAS) AF: 0.111 AC: 575 AN: 5190

South Asian (SAS) AF: 0.149 AC: 718 AN: 4818

European-Finnish (FIN) AF: 0.175 AC: 1839 AN: 10502

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11194 AN: 67950

Other (OTH) AF: 0.160 AC: 336 AN: 2100

Alfa AF: 0.160 Hom.: 2764

Bravo AF: 0.148

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.46
DANN	Benign	0.50
PhyloP100		0.16
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: rs17803698; hg19: chr16-11070289;