16-11148334-G-T

Variant names:

• chr16-11148334-G-T
• rs12927046
• NM_015226.3:c.2642-18054G>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.2642-18054G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,168 control chromosomes in the GnomAD database, including 1,444 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 0.13 (1444 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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.2642-18054G>T		intron	N/A	NP_056041.1
	CLEC16A	NM_001410905.1		c.2636-18054G>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.2642-18054G>T		intron	N/A	ENSP00000387122.1
	CLEC16A	ENST00000904405.1		c.2636-18054G>T		intron	N/A	ENSP00000574464.1
	CLEC16A	ENST00000923410.1		c.2588-18054G>T		intron	N/A	ENSP00000593469.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19450 AN: 152050 Hom.: 1434 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.128 AC: 19496 AN: 152168 Hom.: 1444 Cov.: 32 AF XY: 0.129 AC XY: 9610 AN XY: 74410

African (AFR) AF: 0.199 AC: 8253 AN: 41496

American (AMR) AF: 0.103 AC: 1580 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3468

East Asian (EAS) AF: 0.142 AC: 734 AN: 5184

South Asian (SAS) AF: 0.183 AC: 882 AN: 4820

European-Finnish (FIN) AF: 0.0976 AC: 1034 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0955 AC: 6492 AN: 67988

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.102 Hom.: 1128

Bravo AF: 0.132

Asia WGS AF: 0.172 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.22
DANN	Benign	0.67
PhyloP100		-0.42
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: rs12927046; hg19: chr16-11242191;