16-11001649-C-G

Variant names:

• chr16-11001649-C-G
• rs9940155
• NM_015226.3:c.1072-1425C>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.1072-1425C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,092 control chromosomes in the GnomAD database, including 920 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 0.11 (920 hom., cov: 32)
• Consequence: CLEC16A NM_015226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3	c.1072-1425C>G		intron_variant	Intron 10 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6	c.1072-1425C>G		intron_variant	Intron 10 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4	c.1066-1425C>G		intron_variant	Intron 9 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1	c.1066-1425C>G		intron_variant	Intron 9 of 22			ENSP00000515187.1
CLEC16A	ENST00000494853.1	n.547-1425C>G		intron_variant	Intron 5 of 7	3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16441 AN: 151974 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.108 AC: 16445 AN: 152092 Hom.: 920 Cov.: 32 AF XY: 0.107 AC XY: 7921 AN XY: 74346

African (AFR) AF: 0.128 AC: 5303 AN: 41482

American (AMR) AF: 0.102 AC: 1555 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3468

East Asian (EAS) AF: 0.119 AC: 612 AN: 5160

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4814

European-Finnish (FIN) AF: 0.0792 AC: 839 AN: 10596

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7150 AN: 67972

Other (OTH) AF: 0.117 AC: 246 AN: 2108

Alfa AF: 0.105 Hom.: 111

Bravo AF: 0.112

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.50
PhyloP100		0.082
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: rs9940155; hg19: chr16-11095506;