chr16-11004522-C-G

Variant names:

• chr16-11004522-C-G
• rs723586
• NM_015226.3:c.1303+1217C>G

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+1217C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,074 control chromosomes in the GnomAD database, including 5,748 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 0.27 (5748 hom., cov: 31)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1303+1217C>G		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+1217C>G		intron_variant	Intron 11 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1249+1265C>G		intron_variant	Intron 10 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1297+1217C>G		intron_variant	Intron 10 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.778+1217C>G		intron_variant	Intron 6 of 7	3

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41531 AN: 151954 Hom.: 5745 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.273 AC: 41563 AN: 152074 Hom.: 5748 Cov.: 31 AF XY: 0.271 AC XY: 20156 AN XY: 74336

African (AFR) AF: 0.263 AC: 10923 AN: 41472

American (AMR) AF: 0.261 AC: 3988 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5176

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4822

European-Finnish (FIN) AF: 0.233 AC: 2469 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19618 AN: 67952

Other (OTH) AF: 0.303 AC: 639 AN: 2110

Alfa AF: 0.277 Hom.: 743

Bravo AF: 0.273

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.40
PhyloP100		-0.81
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: rs723586; hg19: chr16-11098379;