rs8062322

Variant names:

• chr16-10998462-C-A
• rs8062322
• NM_015226.3:c.1072-4612C>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.1072-4612C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,070 control chromosomes in the GnomAD database, including 10,311 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 0.36 (10311 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 17 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1072-4612C>A		intron_variant	Intron 10 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1072-4612C>A		intron_variant	Intron 10 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1066-4612C>A		intron_variant	Intron 9 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1066-4612C>A		intron_variant	Intron 9 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.547-4612C>A		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54478 AN: 151950 Hom.: 10287 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.359 AC: 54545 AN: 152070 Hom.: 10311 Cov.: 32 AF XY: 0.356 AC XY: 26474 AN XY: 74354

African (AFR) AF: 0.480 AC: 19911 AN: 41450

American (AMR) AF: 0.291 AC: 4453 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5168

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4822

European-Finnish (FIN) AF: 0.304 AC: 3214 AN: 10576

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21448 AN: 67980

Other (OTH) AF: 0.359 AC: 757 AN: 2110

Alfa AF: 0.333 Hom.: 25512

Bravo AF: 0.359

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		0.25
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: rs8062322; hg19: chr16-11092319;