dbSNP rs16957976: CLEC16A:c.1866+122T>C (chr16-11047464-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015226.3(CLEC16A):c.1866+122T>C 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 522,824 control chromosomes in the GnomAD database, including 3,313 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 0.12 ( 1139 hom., cov: 32)

Exomes 𝑓: 0.10 ( 2174 hom. )

Consequence

CLEC16A
NM_015226.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.337

Publications

13 publications found

Variant links:

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)

CLEC16A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3 link	c.1866+122T>C		intron_variant	Intron 17 of 23	ENST00000409790.6	NP_056041.1	Q2KHT3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC16A	ENST00000409790.6 link	c.1866+122T>C		intron_variant	Intron 17 of 23	5	NM_015226.3	ENSP00000387122.1		Q2KHT3-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18217

AN:

152022

Hom.:

1136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.0972

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.0481

Gnomad FIN

AF:

0.0911

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.133

GnomAD4 exome

AF:

0.103

AC:

38281

AN:

370684

Hom.:

2174

Cov.:

AF XY:

0.102

AC XY:

19363

AN XY:

190624

show subpopulations

African (AFR)

AF:

0.157

AC:

1429

AN:

9082

American (AMR)

AF:

0.116

AC:

990

AN:

8504

Ashkenazi Jewish (ASJ)

AF:

0.0916

AC:

971

AN:

10598

East Asian (EAS)

AF:

0.126

AC:

2954

AN:

23444

South Asian (SAS)

AF:

0.0440

AC:

738

AN:

16758

European-Finnish (FIN)

AF:

0.0942

AC:

2900

AN:

30778

Middle Eastern (MID)

AF:

0.111

AC:

179

AN:

1612

European-Non Finnish (NFE)

AF:

0.103

AC:

25784

AN:

249130

Other (OTH)

AF:

0.112

AC:

2336

AN:

20778

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1606

3213

4819

6426

8032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

462

924

1386

1848

2310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.120

AC:

18234

AN:

152140

Hom.:

1139

Cov.:

AF XY:

0.119

AC XY:

8814

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.160

AC:

6628

AN:

41494

American (AMR)

AF:

0.115

AC:

1752

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0972

AC:

337

AN:

3468

East Asian (EAS)

AF:

0.115

AC:

597

AN:

5170

South Asian (SAS)

AF:

0.0481

AC:

232

AN:

4822

European-Finnish (FIN)

AF:

0.0911

AC:

965

AN:

10592

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7254

AN:

67984

Other (OTH)

AF:

0.133

AC:

281

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

802

1604

2405

3207

4009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.111

Hom.:

1653

Bravo

AF:

0.125

Asia WGS

AF:

0.100

AC:

346

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.7

(source)

DANN

Benign

0.85

PhyloP100

-0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over