chr16-11163079-G-T

Variant names:

• chr16-11163079-G-T
• rs767019
• NM_015226.3:c.2642-3309G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015226.3(CLEC16A):​c.2642-3309G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,076 control chromosomes in the GnomAD database, including 12,879 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 0.41 (12879 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 11 publications found

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 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015226.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2642-3309G>T		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2636-3309G>T		intron	N/A	NP_001397834.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2642-3309G>T		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000703130.1		c.2636-3309G>T		intron	N/A	ENSP00000515187.1
	CLEC16A	ENST00000261657.5	TSL:4	c.215-3309G>T		intron	N/A	ENSP00000261657.5

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61680 AN: 151956 Hom.: 12873 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61697 AN: 152076 Hom.: 12879 Cov.: 32 AF XY: 0.400 AC XY: 29716 AN XY: 74328

African (AFR) AF: 0.406 AC: 16843 AN: 41482

American (AMR) AF: 0.342 AC: 5220 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1700 AN: 3462

East Asian (EAS) AF: 0.168 AC: 872 AN: 5188

South Asian (SAS) AF: 0.477 AC: 2297 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3573 AN: 10558

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29747 AN: 67974

Other (OTH) AF: 0.405 AC: 854 AN: 2108

Alfa AF: 0.418 Hom.: 53677

Bravo AF: 0.401

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.50
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs767019; hg19: chr16-11256936;