rs16957976

Positions:

• chr16-11047464-T-C

Variant summary

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

The NM_015226.3(CLEC16A):​c.1866+122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 522,824 control chromosomes in the GnomAD database, including 3,313 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 0.12 (1139 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2174 hom.)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.1866+122T>C		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1866+122T>C		intron_variant		5	NM_015226.3	A1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18217 AN: 152022 Hom.: 1136 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.0911

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.103 AC: 38281 AN: 370684 Hom.: 2174 Cov.: 6 AF XY: 0.102 AC XY: 19363 AN XY: 190624

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.116

Gnomad4 ASJ exome AF: 0.0916

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.0440

Gnomad4 FIN exome AF: 0.0942

Gnomad4 NFE exome AF: 0.103

Gnomad4 OTH exome AF: 0.112

GnomAD4 genome AF: 0.120 AC: 18234 AN: 152140 Hom.: 1139 Cov.: 32 AF XY: 0.119 AC XY: 8814 AN XY: 74374

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0972

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.0911

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.133

Alfa AF: 0.109 Hom.: 1271

Bravo AF: 0.125

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.85

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: rs16957976; hg19: chr16-11141321;