NM_015226.3:c.2117-26689G>A

Variant names:

• chr16-11093926-G-A
• rs12924729
• NM_015226.3:c.2117-26689G>A

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-26689G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,014 control chromosomes in the GnomAD database, including 9,028 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 0.34 (9028 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 62 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.2117-26689G>A		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.2117-26689G>A		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51914 AN: 151898 Hom.: 9003 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.342 AC: 51989 AN: 152014 Hom.: 9028 Cov.: 31 AF XY: 0.340 AC XY: 25274 AN XY: 74312

African (AFR) AF: 0.391 AC: 16224 AN: 41460

American (AMR) AF: 0.279 AC: 4274 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1112 AN: 5154

South Asian (SAS) AF: 0.396 AC: 1904 AN: 4814

European-Finnish (FIN) AF: 0.330 AC: 3492 AN: 10570

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22573 AN: 67940

Other (OTH) AF: 0.344 AC: 727 AN: 2112

Alfa AF: 0.331 Hom.: 17275

Bravo AF: 0.338

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.35
PhyloP100		-0.68
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: rs12924729; hg19: chr16-11187783;