16-10999464-C-G

Variant names:

• chr16-10999464-C-G
• rs9934231
• NM_015226.3:c.1072-3610C>G

Variant summary

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

The NM_015226.3(CLEC16A):​c.1072-3610C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,992 control chromosomes in the GnomAD database, including 25,253 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 0.56 (25253 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.1072-3610C>G		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.1066-3610C>G		intron	N/A	NP_001397834.1	A0A8V8TR67
	CLEC16A	NM_001243403.2		c.1066-3610C>G		intron	N/A	NP_001230332.1	Q2KHT3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.1072-3610C>G		intron	N/A	ENSP00000387122.1	Q2KHT3-1
	CLEC16A	ENST00000409552.4	TSL:1	c.1066-3610C>G		intron	N/A	ENSP00000386495.3	Q2KHT3-2
	CLEC16A	ENST00000904405.1		c.1066-3610C>G		intron	N/A	ENSP00000574464.1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84475 AN: 151872 Hom.: 25209 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.556 AC: 84577 AN: 151992 Hom.: 25253 Cov.: 32 AF XY: 0.551 AC XY: 40922 AN XY: 74280

African (AFR) AF: 0.776 AC: 32189 AN: 41462

American (AMR) AF: 0.439 AC: 6709 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1487 AN: 5178

South Asian (SAS) AF: 0.663 AC: 3198 AN: 4820

European-Finnish (FIN) AF: 0.420 AC: 4427 AN: 10542

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32892 AN: 67946

Other (OTH) AF: 0.537 AC: 1128 AN: 2102

Alfa AF: 0.375 Hom.: 1079

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.39
PhyloP100		-0.45
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: rs9934231; hg19: chr16-11093321;