chr16-11095291-G-C

Variant names:

• chr16-11095291-G-C
• rs12917716
• NM_015226.3:c.2117-25324G>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.2117-25324G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,988 control chromosomes in the GnomAD database, including 19,998 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 (19998 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 18 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.2117-25324G>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.2117-25324G>C		intron_variant	Intron 19 of 23	5	NM_015226.3	ENSP00000387122.1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76164 AN: 151870 Hom.: 19952 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.502 AC: 76267 AN: 151988 Hom.: 19998 Cov.: 31 AF XY: 0.499 AC XY: 37033 AN XY: 74284

African (AFR) AF: 0.668 AC: 27650 AN: 41418

American (AMR) AF: 0.453 AC: 6912 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2113 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2123 AN: 4826

European-Finnish (FIN) AF: 0.417 AC: 4414 AN: 10576

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29593 AN: 67954

Other (OTH) AF: 0.514 AC: 1087 AN: 2114

Alfa AF: 0.472 Hom.: 2196

Bravo AF: 0.511

Asia WGS AF: 0.488 AC: 1695 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	1.2
DANN	Benign	0.49
PhyloP100		-0.14
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: rs12917716; hg19: chr16-11189148;