rs11643123

Positions:

• chr16-11166583-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2806+31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,534,530 control chromosomes in the GnomAD database, including 12,758 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 0.13 (1263 hom., cov: 32)
  • Exomes 𝑓: 0.12 (11495 hom.)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2806+31A>G		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2806+31A>G		intron_variant		5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000703130.1	c.2800+31A>G		intron_variant				ENSP00000515187.1
CLEC16A	ENST00000261657.5	c.379+31A>G		intron_variant		4		ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19239 AN: 152126 Hom.: 1253 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.130

GnomAD3 exomes AF: 0.134 AC: 25672 AN: 191350 Hom.: 1922 AF XY: 0.142 AC XY: 14892 AN XY: 104776

Gnomad AFR exome AF: 0.134

Gnomad AMR exome AF: 0.0907

Gnomad ASJ exome AF: 0.103

Gnomad EAS exome AF: 0.162

Gnomad SAS exome AF: 0.255

Gnomad FIN exome AF: 0.118

Gnomad NFE exome AF: 0.118

Gnomad OTH exome AF: 0.136

GnomAD4 exome AF: 0.123 AC: 170521 AN: 1382286 Hom.: 11495 Cov.: 31 AF XY: 0.127 AC XY: 86718 AN XY: 680624

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.0894

Gnomad4 ASJ exome AF: 0.0966

Gnomad4 EAS exome AF: 0.138

Gnomad4 SAS exome AF: 0.243

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.127 AC: 19282 AN: 152244 Hom.: 1263 Cov.: 32 AF XY: 0.129 AC XY: 9605 AN XY: 74448

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.137

Alfa AF: 0.118 Hom.: 776

Bravo AF: 0.125

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.35

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: rs11643123; hg19: chr16-11260440; COSMIC: COSV55489589;