rs8062322

Positions:

• chr16-10998462-C-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1072-4612C>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1072-4612C>A		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.1066-4612C>A		intron_variant		1
CLEC16A	ENST00000703130.1	c.1066-4612C>A		intron_variant				P4
CLEC16A	ENST00000494853.1	n.547-4612C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.359

Alfa AF: 0.325 Hom.: 16116

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs8062322; hg19: chr16-11092319;