16-11003622-C-T

Variant names:

• chr16-11003622-C-T
• rs9925481
• NM_015226.3:c.1303+317C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.94).
• 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 rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1303+317C>T		intron_variant	Intron 11 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1303+317C>T		intron_variant	Intron 11 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1249+365C>T		intron_variant	Intron 10 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1297+317C>T		intron_variant	Intron 10 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.778+317C>T		intron_variant	Intron 6 of 7	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

African (AFR) AF: 0.209 AC: 8668 AN: 41426

American (AMR) AF: 0.0942 AC: 1441 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5182

South Asian (SAS) AF: 0.0419 AC: 202 AN: 4818

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0721 AC: 4900 AN: 68008

Other (OTH) AF: 0.115 AC: 243 AN: 2108

Alfa AF: 0.0800 Hom.: 287

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
PhyloP100		-0.41
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: rs9925481; hg19: chr16-11097479;