16-11001649-C-G

Position:

• chr16-11001649-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.1072-1425C>G 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 152,092 control chromosomes in the GnomAD database, including 920 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 0.11 (920 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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]

CLEC16A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1072-1425C>G		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1072-1425C>G		intron_variant		5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1066-1425C>G		intron_variant		1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1066-1425C>G		intron_variant				ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.547-1425C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16441 AN: 151974 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.108 AC: 16445 AN: 152092 Hom.: 920 Cov.: 32 AF XY: 0.107 AC XY: 7921 AN XY: 74346

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0442

Gnomad4 FIN AF: 0.0792

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.117

Alfa AF: 0.105 Hom.: 111

Bravo AF: 0.112

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.50

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: rs9940155; hg19: chr16-11095506;