5-37249431-C-G

Variant names:

• chr5-37249431-C-G
• rs80164363
• ENST00000650795.2:n.202+210C>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.115

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPLANE1	NM_001384732.1	c.-234G>C		upstream_gene_variant		ENST00000651892.2	NP_001371661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPLANE1	ENST00000651892.2	c.-234G>C		upstream_gene_variant			NM_001384732.1	ENSP00000498265.2

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11897 AN: 152084 Hom.: 701 Cov.: 33

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: 4 AN: 144 Hom.: 0 Cov.: 0 AF XY: 0.0273 AC XY: 3 AN XY: 110

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0308

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0783 AC: 11920 AN: 152192 Hom.: 707 Cov.: 33 AF XY: 0.0780 AC XY: 5802 AN XY: 74388

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0690

Alfa AF: 0.0297 Hom.: 21

Bravo AF: 0.0779

Asia WGS AF: 0.0830 AC: 288 AN: 3462

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Familial aplasia of the vermis Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs80164363; hg19: chr5-37249533;