rs17477326

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018246.3(CCDC25):​c.551+2394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,100 control chromosomes in the GnomAD database, including 8,001 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 0.30 ( 8001 hom., cov: 33)

Consequence

CCDC25
NM_018246.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.146

Publications

10 publications found
Variant links:
Genes affected
CCDC25 (HGNC:25591): (coiled-coil domain containing 25) Enables DNA binding activity. Involved in positive regulation of cell motility. Located in endomembrane system. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC25NM_018246.3 linkc.551+2394C>T intron_variant Intron 7 of 8 ENST00000356537.9 NP_060716.2 Q86WR0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC25ENST00000356537.9 linkc.551+2394C>T intron_variant Intron 7 of 8 1 NM_018246.3 ENSP00000348933.4 Q86WR0-1

Frequencies

GnomAD3 genomes
AF:
0.300
AC:
45625
AN:
151982
Hom.:
8006
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.424
Gnomad AMR
AF:
0.312
Gnomad ASJ
AF:
0.480
Gnomad EAS
AF:
0.119
Gnomad SAS
AF:
0.347
Gnomad FIN
AF:
0.435
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.383
Gnomad OTH
AF:
0.323
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.300
AC:
45642
AN:
152100
Hom.:
8001
Cov.:
33
AF XY:
0.304
AC XY:
22597
AN XY:
74334
show subpopulations
African (AFR)
AF:
0.124
AC:
5125
AN:
41496
American (AMR)
AF:
0.311
AC:
4759
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.480
AC:
1663
AN:
3468
East Asian (EAS)
AF:
0.120
AC:
619
AN:
5160
South Asian (SAS)
AF:
0.349
AC:
1681
AN:
4822
European-Finnish (FIN)
AF:
0.435
AC:
4602
AN:
10568
Middle Eastern (MID)
AF:
0.398
AC:
117
AN:
294
European-Non Finnish (NFE)
AF:
0.383
AC:
26010
AN:
67980
Other (OTH)
AF:
0.321
AC:
679
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1592
3183
4775
6366
7958
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
462
924
1386
1848
2310
<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:
0.359
Hom.:
17091
Bravo
AF:
0.280
Asia WGS
AF:
0.220
AC:
769
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.2
DANN
Benign
0.79
PhyloP100
-0.15
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs17477326; hg19: chr8-27603200; API