chr16-11100914-C-T

Variant names:

• chr16-11100914-C-T
• rs12927355
• NM_015226.3:c.2117-19701C>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.2117-19701C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,916 control chromosomes in the GnomAD database, including 6,780 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 0.30 (6780 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 41 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 = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2117-19701C>T		intron_variant	Intron 19 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2117-19701C>T		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44841 AN: 151798 Hom.: 6760 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.296 AC: 44900 AN: 151916 Hom.: 6780 Cov.: 32 AF XY: 0.295 AC XY: 21892 AN XY: 74222

African (AFR) AF: 0.242 AC: 10015 AN: 41426

American (AMR) AF: 0.260 AC: 3976 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3464

East Asian (EAS) AF: 0.189 AC: 978 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1821 AN: 4804

European-Finnish (FIN) AF: 0.329 AC: 3461 AN: 10532

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22239 AN: 67930

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.260 Hom.: 1256

Bravo AF: 0.286

Asia WGS AF: 0.300 AC: 1042 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	0.23
DANN	Benign	0.53
PhyloP100		-0.86
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: rs12927355; hg19: chr16-11194771;