dbSNP rs80164363: CPLANE1-AS1:n.236+210C>G (chr5-37249431-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NR_134263.1(CPLANE1-AS1):n.176+210C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 152,336 control chromosomes in the GnomAD database, including 707 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 707 hom., cov: 33)

Exomes 𝑓: 0.028 ( 0 hom. )

Consequence

CPLANE1-AS1
NR_134263.1 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.115

Publications

2 publications found

Variant links:

Genes affected

CPLANE1-AS1 (HGNC:56117): (CPLANE1 antisense RNA 1)

CPLANE1-AS1 links:

CPLANE1 (HGNC:25801): (ciliogenesis and planar polarity effector complex subunit 1) The protein encoded by this gene has putative coiled-coil domains and may be a transmembrane protein. Defects in this gene are a cause of Joubert syndrome (JBTS). [provided by RefSeq, May 2012]

CPLANE1 Gene-Disease associations (from GenCC):

Joubert syndrome 17
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Illumina
orofaciodigital syndrome type 6
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
Joubert syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CPLANE1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-37249431-C-G is Benign according to our data. Variant chr5-37249431-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 369472.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_134263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CPLANE1-AS1	NR_134263.1		n.176+210C>G	intron	N/A
CPLANE1	NM_001384732.1	MANE Select	c.-234G>C	upstream_gene	N/A	NP_001371661.1	A0A494BZW6
CPLANE1	NM_023073.4		c.-234G>C	upstream_gene	N/A	NP_075561.3

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
CPLANE1-AS1	ENST00000650795.3	n.236+210C>G	intron	N/A
CPLANE1-AS1	ENST00000651145.2	n.243+210C>G	intron	N/A
CPLANE1-AS1	ENST00000659285.1	n.196+210C>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0782

AC:

11897

AN:

152084

Hom.:

701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0355

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.0373

Gnomad SAS

AF:

0.0807

Gnomad FIN

AF:

0.0627

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0447

Gnomad OTH

AF:

0.0635

GnomAD4 exome

AF:

0.0278

AC:

AN:

144

Hom.:

Cov.:

AF XY:

0.0273

AC XY:

AN XY:

110

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0308

AC:

AN:

130

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0783

AC:

11920

AN:

152192

Hom.:

707

Cov.:

AF XY:

0.0780

AC XY:

5802

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.162

AC:

6737

AN:

41546

American (AMR)

AF:

0.0354

AC:

542

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0487

AC:

169

AN:

3472

East Asian (EAS)

AF:

0.0377

AC:

194

AN:

5152

South Asian (SAS)

AF:

0.0805

AC:

389

AN:

4830

European-Finnish (FIN)

AF:

0.0627

AC:

665

AN:

10600

Middle Eastern (MID)

AF:

0.0274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0447

AC:

3037

AN:

67974

Other (OTH)

AF:

0.0690

AC:

146

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

565

1130

1694

2259

2824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0297

Hom.:

Bravo

AF:

0.0779

Asia WGS

AF:

0.0830

AC:

288

AN:

3462

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Joubert syndrome (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.0

(source)

DANN

Benign

0.47

PhyloP100

-0.12

PromoterAI

-0.092

Neutral

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over