16-10946769-A-T

Position:

• chr16-10946769-A-T

Variant summary

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

The NM_015226.3(CLEC16A):​c.80+1972A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,098 control chromosomes in the GnomAD database, including 39,909 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 0.71 (39909 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.80+1972A>T		intron_variant		ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.80+1972A>T		intron_variant		5	NM_015226.3	ENSP00000387122	A1
CLEC16A	ENST00000409552.4	c.80+1972A>T		intron_variant		1		ENSP00000386495
CLEC16A	ENST00000703130.1	c.80+1972A>T		intron_variant				ENSP00000515187	P4

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107442 AN: 151980 Hom.: 39907 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.707 AC: 107482 AN: 152098 Hom.: 39909 Cov.: 32 AF XY: 0.712 AC XY: 52920 AN XY: 74358

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.721

Alfa AF: 0.739 Hom.: 5326

Bravo AF: 0.689

Asia WGS AF: 0.761 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.76

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: rs12922318; hg19: chr16-11040626;