rs723586

chr16-11004522-C-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• 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/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1303+1217C>G		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1303+1217C>G		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000409552.4	c.1249+1265C>G		intron_variant		1
CLEC16A	ENST00000703130.1	c.1297+1217C>G		intron_variant				P4
CLEC16A	ENST00000494853.1	n.778+1217C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.303

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

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: rs723586; hg19: chr16-11098379;