16-11158972-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.2642-7416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,532 control chromosomes in the GnomAD database, including 38,767 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 0.70 (38767 hom., cov: 30)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

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]

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC16A	NM_015226.3	c.2642-7416C>T		intron_variant		ENST00000409790.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC16A	ENST00000409790.6	c.2642-7416C>T		intron_variant		5	NM_015226.3	A1
	ENST00000667071.1	n.174-3247G>A		intron_variant, non_coding_transcript_variant
CLEC16A	ENST00000261657.5	c.216-7416C>T		intron_variant		4
CLEC16A	ENST00000703130.1	c.2636-7416C>T		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106510 AN: 151422 Hom.: 38719 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.704 AC: 106609 AN: 151532 Hom.: 38767 Cov.: 30 AF XY: 0.697 AC XY: 51562 AN XY: 73938

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.696

Alfa AF: 0.654 Hom.: 11834

Bravo AF: 0.706

Asia WGS AF: 0.615 AC: 2138 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
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: rs28087; hg19: chr16-11252829;