dbSNP rs10180793: CERKL:p.Asp502Asp (chr2-181539124-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_201548.5(CERKL):c.1506C>T(p.Asp502Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,608,470 control chromosomes in the GnomAD database, including 801,911 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.99 ( 75051 hom., cov: 31)

Exomes 𝑓: 1.0 ( 726860 hom. )

Consequence

CERKL
NM_201548.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: 0.749

Publications

19 publications found

Variant links:

Genes affected

CERKL (HGNC:21699): (ceramide kinase like) This gene was initially identified as a locus (RP26) associated with an autosomal recessive form of retinitis pigmentosa (arRP) disease. This gene encodes a protein with ceramide kinase-like domains, however, the protein does not phosphorylate ceramide and its target substrate is currently unknown. This protein may be a negative regulator of apoptosis in photoreceptor cells. Mutations in this gene cause a form of retinitis pigmentosa characterized by autosomal recessive cone and rod dystrophy (arCRD). Alternative splicing of this gene results in multiple transcript variants encoding different isoforms and non-coding transcripts.[provided by RefSeq, May 2010]

CERKL links:

ITGA4 (HGNC:6140): (integrin subunit alpha 4) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function in cell surface adhesion and signaling. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 4 subunit. This subunit associates with a beta 1 or beta 7 subunit to form an integrin that may play a role in cell motility and migration. This integrin is a therapeutic target for the treatment of multiple sclerosis, Crohn's disease and inflammatory bowel disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

ITGA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 2-181539124-G-A is Benign according to our data. Variant chr2-181539124-G-A is described in ClinVar as Benign. ClinVar VariationId is 166844.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.749 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201548.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CERKL	NM_201548.5	MANE Select	c.1506C>T	p.Asp502Asp	synonymous	Exon 12 of 13	NP_963842.1
CERKL	NM_001030311.3		c.1584C>T	p.Asp528Asp	synonymous	Exon 13 of 14	NP_001025482.1
CERKL	NM_001160277.2		c.1452C>T	p.Asp484Asp	synonymous	Exon 12 of 13	NP_001153749.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CERKL	ENST00000410087.8	TSL:1 MANE Select	c.1506C>T	p.Asp502Asp	synonymous	Exon 12 of 13	ENSP00000386725.3
CERKL	ENST00000339098.9	TSL:1	c.1584C>T	p.Asp528Asp	synonymous	Exon 13 of 14	ENSP00000341159.5
CERKL	ENST00000374970.6	TSL:1	c.1299C>T	p.Asp433Asp	synonymous	Exon 10 of 11	ENSP00000364109.2

Frequencies

GnomAD3 genomes

AF:

0.993

AC:

151050

AN:

152134

Hom.:

75001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.976

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.995

Gnomad ASJ

AF:

0.996

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.995

GnomAD2 exomes

AF:

0.998

AC:

250751

AN:

251272

AF XY:

0.998

show subpopulations

Gnomad AFR exome

AF:

0.976

Gnomad AMR exome

AF:

0.998

Gnomad ASJ exome

AF:

0.995

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.999

GnomAD4 exome

AF:

0.999

AC:

1454956

AN:

1456218

Hom.:

726860

Cov.:

AF XY:

0.999

AC XY:

724216

AN XY:

724762

show subpopulations

African (AFR)

AF:

0.976

AC:

32520

AN:

33326

American (AMR)

AF:

0.998

AC:

44638

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.996

AC:

25956

AN:

26072

East Asian (EAS)

AF:

1.00

AC:

39585

AN:

39586

South Asian (SAS)

AF:

1.00

AC:

86107

AN:

86126

European-Finnish (FIN)

AF:

1.00

AC:

53386

AN:

53386

Middle Eastern (MID)

AF:

0.998

AC:

5744

AN:

5756

European-Non Finnish (NFE)

AF:

1.00

AC:

1106999

AN:

1107066

Other (OTH)

AF:

0.997

AC:

60021

AN:

60186

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

130

196

261

326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21546

43092

64638

86184

107730

<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:

0.993

AC:

151159

AN:

152252

Hom.:

75051

Cov.:

AF XY:

0.993

AC XY:

73902

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.976

AC:

40565

AN:

41554

American (AMR)

AF:

0.995

AC:

15196

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.996

AC:

3457

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5187

AN:

5188

South Asian (SAS)

AF:

1.00

AC:

4822

AN:

4822

European-Finnish (FIN)

AF:

1.00

AC:

10612

AN:

10612

Middle Eastern (MID)

AF:

1.00

AC:

294

AN:

294

European-Non Finnish (NFE)

AF:

1.00

AC:

68013

AN:

68020

Other (OTH)

AF:

0.995

AC:

2103

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

111

167

222

278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

914

1828

2742

3656

4570

<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:

0.997

Hom.:

144230

Bravo

AF:

0.992

Asia WGS

AF:

0.997

AC:

3464

AN:

3476

EpiCase

AF:

1.00

EpiControl

AF:

1.00

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

not provided (3)

Retinitis pigmentosa 26 (2)

Retinitis pigmentosa (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.0

(source)

DANN

Benign

0.76

PhyloP100

0.75

Mutation Taster

=79/21

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