dbSNP rs16957849: CLEC16A:c.598+220T>C (chr16-10971450-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.598+220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 628,106 control chromosomes in the GnomAD database, including 14,954 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 0.21 ( 3566 hom., cov: 32)

Exomes 𝑓: 0.21 ( 11388 hom. )

Consequence

CLEC16A
NM_015226.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

Publications

9 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 (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC16A	NM_015226.3 link	c.598+220T>C		intron_variant	Intron 5 of 23	ENST00000409790.6	NP_056041.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
CLEC16A	ENST00000409790.6 link	c.598+220T>C	intron_variant	Intron 5 of 23	5	NM_015226.3	ENSP00000387122.1
CLEC16A	ENST00000409552.4 link	c.598+220T>C	intron_variant	Intron 5 of 20	1		ENSP00000386495.3
CLEC16A	ENST00000703130.1 link	c.598+220T>C	intron_variant	Intron 5 of 22			ENSP00000515187.1

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31865

AN:

152042

Hom.:

3559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.0841

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.188

GnomAD4 exome

AF:

0.214

AC:

101907

AN:

475946

Hom.:

11388

AF XY:

0.216

AC XY:

48312

AN XY:

224040

show subpopulations

African (AFR)

AF:

0.281

AC:

2478

AN:

8830

American (AMR)

AF:

0.126

AC:

AN:

540

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

397

AN:

2890

East Asian (EAS)

AF:

0.0750

AC:

144

AN:

1920

South Asian (SAS)

AF:

0.302

AC:

2823

AN:

9344

European-Finnish (FIN)

AF:

0.199

AC:

AN:

176

Middle Eastern (MID)

AF:

0.202

AC:

197

AN:

974

European-Non Finnish (NFE)

AF:

0.212

AC:

92361

AN:

435740

Other (OTH)

AF:

0.219

AC:

3404

AN:

15532

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

3804

7608

11413

15217

19021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4414

8828

13242

17656

22070

<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:

0.210

AC:

31894

AN:

152160

Hom.:

3566

Cov.:

AF XY:

0.207

AC XY:

15413

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.270

AC:

11210

AN:

41474

American (AMR)

AF:

0.156

AC:

2380

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

525

AN:

3466

East Asian (EAS)

AF:

0.0839

AC:

435

AN:

5182

South Asian (SAS)

AF:

0.300

AC:

1449

AN:

4822

European-Finnish (FIN)

AF:

0.156

AC:

1656

AN:

10606

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.199

AC:

13565

AN:

67996

Other (OTH)

AF:

0.186

AC:

394

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1266

2533

3799

5066

6332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.201

Hom.:

6386

Bravo

AF:

0.209

Asia WGS

AF:

0.172

AC:

599

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

1.1

(source)

DANN

Benign

0.59

PhyloP100

0.15

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