rs3960630

chr16-11177047-C-Achr16-11177047-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):c.2807-1288C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,104 control chromosomes in the GnomAD database, including 4,811 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 0.25 (4811 hom., cov: 33)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278

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 = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2807-1288C>A		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2807-1288C>A		intron_variant		5	NM_015226.3	A1
CLEC16A	ENST00000261657.5	c.*48-1288C>A		intron_variant		4
CLEC16A	ENST00000703130.1	c.2801-1288C>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37534 AN: 151986 Hom.: 4802 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.247 AC: 37560 AN: 152104 Hom.: 4811 Cov.: 33 AF XY: 0.247 AC XY: 18377 AN XY: 74370

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.237

Alfa AF: 0.225 Hom.: 5469

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	8.4
Dann	Benign	0.62

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: rs3960630; hg19: chr16-11270904;