16-11003622-C-T

Variant summary

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

The NM_015226.3(CLEC16A):c.1303+317C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,096 control chromosomes in the GnomAD database, including 1,211 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 0.11 (1211 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1303+317C>T		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1303+317C>T		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.1249+365C>T		intron_variant		1
CLEC16A	ENST00000703130.1	c.1297+317C>T		intron_variant				P4
CLEC16A	ENST00000494853.1	n.778+317C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16970 AN: 151978 Hom.: 1207 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0945

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.112 AC: 17003 AN: 152096 Hom.: 1211 Cov.: 31 AF XY: 0.110 AC XY: 8207 AN XY: 74348

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0525 Hom.: 79

Bravo AF: 0.121

Asia WGS AF: 0.101 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.6
Dann	Benign	0.60

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: rs9925481; hg19: chr16-11097479;