16-10948537-G-A

Variant names:

• chr16-10948537-G-A
• rs8055876
• NM_015226.3:c.80+3740G>A

Variant summary

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

The NM_015226.3(CLEC16A):​c.80+3740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,130 control chromosomes in the GnomAD database, including 2,115 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 0.15 (2115 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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.80+3740G>A		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.80+3740G>A		intron	N/A	NP_001397834.1
	CLEC16A	NM_001243403.2		c.80+3740G>A		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.80+3740G>A		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000409552.4	TSL:1	c.80+3740G>A		intron	N/A	ENSP00000386495.3
	CLEC16A	ENST00000703130.1		c.80+3740G>A		intron	N/A	ENSP00000515187.1

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22979 AN: 152012 Hom.: 2110 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.151 AC: 23003 AN: 152130 Hom.: 2115 Cov.: 32 AF XY: 0.151 AC XY: 11207 AN XY: 74382

African (AFR) AF: 0.248 AC: 10300 AN: 41452

American (AMR) AF: 0.105 AC: 1610 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3470

East Asian (EAS) AF: 0.0855 AC: 442 AN: 5168

South Asian (SAS) AF: 0.267 AC: 1285 AN: 4816

European-Finnish (FIN) AF: 0.0766 AC: 812 AN: 10604

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7813 AN: 67998

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.125 Hom.: 5866

Bravo AF: 0.155

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.64
PhyloP100		-1.1
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: rs8055876; hg19: chr16-11042394;