rs12599402

Variant names:

• chr16-11096031-T-C
• rs12599402
• NM_015226.3:c.2117-24584T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2117-24584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,754 control chromosomes in the GnomAD database, including 20,108 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 0.50 (20108 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 44 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2117-24584T>C		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.2117-24584T>C		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76371 AN: 151636 Hom.: 20061 Cov.: 30

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.504 AC: 76476 AN: 151754 Hom.: 20108 Cov.: 30 AF XY: 0.501 AC XY: 37130 AN XY: 74130

African (AFR) AF: 0.668 AC: 27626 AN: 41360

American (AMR) AF: 0.456 AC: 6950 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1847 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2087 AN: 5152

South Asian (SAS) AF: 0.442 AC: 2115 AN: 4790

European-Finnish (FIN) AF: 0.421 AC: 4431 AN: 10526

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29805 AN: 67896

Other (OTH) AF: 0.518 AC: 1090 AN: 2106

Alfa AF: 0.455 Hom.: 70153

Bravo AF: 0.513

Asia WGS AF: 0.489 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.35
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: rs12599402; hg19: chr16-11189888;