rs45437097

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001080414.4(CCDC88C):c.114C>T(p.Tyr38Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,612,464 control chromosomes in the GnomAD database, including 41,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2774 hom., cov: 32)

Exomes 𝑓: 0.22 ( 38875 hom. )

Consequence

CCDC88C
NM_001080414.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.461

Variant links:

Genes affected

CCDC88C (HGNC:19967): (coiled-coil domain containing 88C) This gene encodes a ubiquitously expressed coiled-coil domain-containing protein that interacts with the dishevelled protein and is a negative regulator of the Wnt signalling pathway. The protein encoded by this gene has a PDZ-domain binding motif in its C-terminus with which it interacts with the dishevelled protein. Dishevelled is a scaffold protein involved in the regulation of the Wnt signaling pathway. The Wnt signaling pathway plays an important role in embryonic development, tissue maintenance, and cancer progression. Mutations in this gene cause autosomal recessive, primary non-syndromic congenital hydrocephalus; a condition characterized by excessive accumulation of cerebrospinal fluid in the ventricles of the brain. [provided by RefSeq, Jan 2013]

CCDC88C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 14-91416785-G-A is Benign according to our data. Variant chr14-91416785-G-A is described in ClinVar as [Benign]. Clinvar id is 158090.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.461 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC88C	NM_001080414.4 link	c.114C>T	p.Tyr38Tyr	synonymous_variant	Exon 2 of 30	ENST00000389857.11	NP_001073883.2	Q9P219-1B4DZB8
CCDC88C	XM_011536796.3 link	c.6C>T	p.Tyr2Tyr	synonymous_variant	Exon 2 of 30		XP_011535098.1
CCDC88C	NR_189158.1 link	n.244C>T		non_coding_transcript_exon_variant	Exon 2 of 31
CCDC88C	NR_189159.1 link	n.244C>T		non_coding_transcript_exon_variant	Exon 2 of 31

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC88C	ENST00000389857.11 link	c.114C>T	p.Tyr38Tyr	synonymous_variant	Exon 2 of 30	5	NM_001080414.4	ENSP00000374507.6		Q9P219-1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25993

AN:

152006

Hom.:

2778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0814

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.180

Gnomad EAS

AF:

0.0249

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.171

AC:

42367

AN:

247748

Hom.:

4348

AF XY:

0.175

AC XY:

23562

AN XY:

134732

show subpopulations

Gnomad AFR exome

AF:

0.0796

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.180

Gnomad EAS exome

AF:

0.0270

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.239

Gnomad OTH exome

AF:

0.187

GnomAD4 exome

AF:

0.222

AC:

324461

AN:

1460342

Hom.:

38875

Cov.:

AF XY:

0.220

AC XY:

159505

AN XY:

726512

show subpopulations

Gnomad4 AFR exome

AF:

0.0721

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.0335

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.251

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.171

AC:

25989

AN:

152122

Hom.:

2774

Cov.:

AF XY:

0.163

AC XY:

12125

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0812

Gnomad4 AMR

AF:

0.150

Gnomad4 ASJ

AF:

0.180

Gnomad4 EAS

AF:

0.0249

Gnomad4 SAS

AF:

0.130

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.165

Alfa

AF:

0.202

Hom.:

2184

Bravo

AF:

0.164

Asia WGS

AF:

0.0760

AC:

263

AN:

3478

EpiCase

AF:

0.234

EpiControl

AF:

0.229

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Apr 08, 2013

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Spinocerebellar ataxia type 40

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hydrocephalus, nonsyndromic, autosomal recessive 1

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: 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

-0.49

CADD

Benign

DANN

Benign

0.92

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over