16-11113865-T-C

Variant names:

• chr16-11113865-T-C
• rs7203150
• NM_015226.3:c.2117-6750T>C

Variant summary

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

The NM_015226.3(CLEC16A):​c.2117-6750T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,972 control chromosomes in the GnomAD database, including 19,513 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 0.49 (19513 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 18 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=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 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.2117-6750T>C		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2111-6750T>C		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.2063-6750T>C		intron	N/A	NP_001230332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2117-6750T>C		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.2063-6750T>C		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.2111-6750T>C		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75032 AN: 151854 Hom.: 19471 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.494 AC: 75130 AN: 151972 Hom.: 19513 Cov.: 32 AF XY: 0.489 AC XY: 36332 AN XY: 74282

African (AFR) AF: 0.666 AC: 27610 AN: 41432

American (AMR) AF: 0.405 AC: 6185 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1846 AN: 3460

East Asian (EAS) AF: 0.354 AC: 1830 AN: 5170

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4814

European-Finnish (FIN) AF: 0.404 AC: 4262 AN: 10546

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29703 AN: 67958

Other (OTH) AF: 0.504 AC: 1065 AN: 2112

Alfa AF: 0.429 Hom.: 6347

Bravo AF: 0.501

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.57
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: rs7203150; hg19: chr16-11207722;