rs11643123

Variant names:

• chr16-11166583-A-G
• rs11643123
• NM_015226.3:c.2806+31A>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.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
• Publications: 8 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2806+31A>G		intron_variant	Intron 23 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2806+31A>G		intron_variant	Intron 23 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000703130.1	c.2800+31A>G		intron_variant	Intron 22 of 22			ENSP00000515187.1
CLEC16A	ENST00000261657.5	c.379+31A>G		intron_variant	Intron 3 of 4	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

GnomAD2 exomes AF: 0.134 AC: 25672 AN: 191350 AF XY: 0.142

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 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

African (AFR) AF: 0.146 AC: 4572 AN: 31400

American (AMR) AF: 0.0894 AC: 3287 AN: 36758

Ashkenazi Jewish (ASJ) AF: 0.0966 AC: 2262 AN: 23426

East Asian (EAS) AF: 0.138 AC: 5016 AN: 36452

South Asian (SAS) AF: 0.243 AC: 18749 AN: 77270

European-Finnish (FIN) AF: 0.112 AC: 4728 AN: 42294

Middle Eastern (MID) AF: 0.173 AC: 938 AN: 5422

European-Non Finnish (NFE) AF: 0.115 AC: 123708 AN: 1071906

Other (OTH) AF: 0.127 AC: 7261 AN: 57358

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

African (AFR) AF: 0.138 AC: 5739 AN: 41550

American (AMR) AF: 0.108 AC: 1648 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.163 AC: 844 AN: 5178

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1281 AN: 10614

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7922 AN: 67996

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.120 Hom.: 957

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
PhyloP100		-2.2
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: rs11643123; hg19: chr16-11260440; COSMIC: COSV55489589;