rs17803698

Variant names:

• chr16-10976432-A-G
• rs17803698
• NM_015226.3:c.729-793A>G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.729-793A>G		intron_variant	Intron 7 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.729-793A>G		intron_variant	Intron 7 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.723-793A>G		intron_variant	Intron 6 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.723-793A>G		intron_variant	Intron 6 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.204-793A>G		intron_variant	Intron 2 of 7	3

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.160

Alfa AF: 0.162 Hom.: 2144

Bravo AF: 0.148

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.46
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs17803698; hg19: chr16-11070289;