Genetic Variant CLEC16A:c.2807-22C>T (chr16-11178313-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_015226.3(CLEC16A):c.2807-22C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 1,583,626 control chromosomes in the GnomAD database, including 215 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 0.012 ( 22 hom., cov: 33)

Exomes 𝑓: 0.015 ( 193 hom. )

Consequence

CLEC16A
NM_015226.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.69

Publications

2 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=-0.92).

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0115 (1753/152298) while in subpopulation AMR AF = 0.0205 (313/15302). AF 95% confidence interval is 0.0186. There are 22 homozygotes in GnomAd4. There are 825 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 22 Unknown gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLEC16A	NM_015226.3	MANE Select	c.2807-22C>T		intron	N/A	NP_056041.1	Q2KHT3-1
	CLEC16A	NM_001410905.1		c.2801-22C>T		intron	N/A	NP_001397834.1	A0A8V8TR67

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CLEC16A	ENST00000409790.6	TSL:5 MANE Select	c.2807-22C>T	intron	N/A	ENSP00000387122.1	Q2KHT3-1
CLEC16A	ENST00000904405.1		c.2921-22C>T	intron	N/A	ENSP00000574464.1
CLEC16A	ENST00000923410.1		c.2873-22C>T	intron	N/A	ENSP00000593469.1

Frequencies

GnomAD3 genomes

AF:

0.0115

AC:

1753

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00331

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0205

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0168

Gnomad OTH

AF:

0.0129

GnomAD2 exomes

AF:

0.0105

AC:

2485

AN:

237350

AF XY:

0.0108

show subpopulations

Gnomad AFR exome

AF:

0.00253

Gnomad AMR exome

AF:

0.00883

Gnomad ASJ exome

AF:

0.00956

Gnomad EAS exome

AF:

0.0000558

Gnomad FIN exome

AF:

0.00254

Gnomad NFE exome

AF:

0.0160

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.0155

AC:

22164

AN:

1431328

Hom.:

193

Cov.:

AF XY:

0.0152

AC XY:

10728

AN XY:

707932

show subpopulations

African (AFR)

AF:

0.00206

AC:

AN:

33054

American (AMR)

AF:

0.00892

AC:

391

AN:

43832

Ashkenazi Jewish (ASJ)

AF:

0.00972

AC:

241

AN:

24806

East Asian (EAS)

AF:

0.000102

AC:

AN:

39232

South Asian (SAS)

AF:

0.00824

AC:

685

AN:

83082

European-Finnish (FIN)

AF:

0.00262

AC:

136

AN:

51970

Middle Eastern (MID)

AF:

0.00707

AC:

AN:

5654

European-Non Finnish (NFE)

AF:

0.0180

AC:

19672

AN:

1090584

Other (OTH)

AF:

0.0157

AC:

927

AN:

59114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1132

2264

3397

4529

5661

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

748

1496

2244

2992

3740

<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:

0.0115

AC:

1753

AN:

152298

Hom.:

Cov.:

AF XY:

0.0111

AC XY:

825

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.00330

AC:

137

AN:

41568

American (AMR)

AF:

0.0205

AC:

313

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00980

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00539

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00151

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0168

AC:

1145

AN:

68016

Other (OTH)

AF:

0.0128

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

175

263

350

438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00773

Hom.:

Bravo

AF:

0.0119

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.9

(source)

DANN

Benign

0.61

PhyloP100

1.7

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over