rs7203459

Positions:

• chr16-11136846-T-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2641+10700T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,156 control chromosomes in the GnomAD database, including 4,196 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 0.23 (4196 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2641+10700T>C		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2641+10700T>C		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35161 AN: 152038 Hom.: 4196 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.231 AC: 35161 AN: 152156 Hom.: 4196 Cov.: 33 AF XY: 0.229 AC XY: 16998 AN XY: 74380

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.251

Alfa AF: 0.258 Hom.: 5102

Bravo AF: 0.224

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.71

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: rs7203459; hg19: chr16-11230703;