16-10971450-T-C

Position:

• chr16-10971450-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.598+220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 628,106 control chromosomes in the GnomAD database, including 14,954 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 0.21 (3566 hom., cov: 32)
  • Exomes 𝑓: 0.21 (11388 hom.)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

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 (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.598+220T>C		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.598+220T>C		intron_variant		5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.598+220T>C		intron_variant		1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.598+220T>C		intron_variant				ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31865 AN: 152042 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.214 AC: 101907 AN: 475946 Hom.: 11388 AF XY: 0.216 AC XY: 48312 AN XY: 224040

Gnomad4 AFR exome AF: 0.281

Gnomad4 AMR exome AF: 0.126

Gnomad4 ASJ exome AF: 0.137

Gnomad4 EAS exome AF: 0.0750

Gnomad4 SAS exome AF: 0.302

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.210 AC: 31894 AN: 152160 Hom.: 3566 Cov.: 32 AF XY: 0.207 AC XY: 15413 AN XY: 74400

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0839

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.186

Alfa AF: 0.199 Hom.: 4593

Bravo AF: 0.209

Asia WGS AF: 0.172 AC: 599 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	1.1
DANN	Benign	0.59

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: rs16957849; hg19: chr16-11065307;