17-30837005-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024857.5(ATAD5):c.1968-201C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000461 in 151,870 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000046 ( 0 hom., cov: 31)
Consequence
ATAD5
NM_024857.5 intron
NM_024857.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.62
Publications
49 publications found
Genes affected
ATAD5 (HGNC:25752): (ATPase family AAA domain containing 5) Enables DNA clamp unloader activity. Involved in DNA clamp unloading; positive regulation of DNA replication; and positive regulation of cell cycle G2/M phase transition. Part of Elg1 RFC-like complex. Biomarker of neurilemmoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATAD5 | ENST00000321990.5 | c.1968-201C>G | intron_variant | Intron 2 of 22 | 1 | NM_024857.5 | ENSP00000313171.4 | |||
ATAD5 | ENST00000578295.5 | n.1968-201C>G | intron_variant | Intron 2 of 14 | 1 | ENSP00000463102.1 | ||||
ENSG00000265334 | ENST00000580873.1 | n.334-2376G>C | intron_variant | Intron 1 of 1 | 2 | |||||
ATAD5 | ENST00000585133.1 | n.841-201C>G | intron_variant | Intron 1 of 12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151870Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
7
AN:
151870
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151870Hom.: 0 Cov.: 31 AF XY: 0.0000405 AC XY: 3AN XY: 74158 show subpopulations
GnomAD4 genome
AF:
AC:
7
AN:
151870
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
74158
show subpopulations
African (AFR)
AF:
AC:
3
AN:
41328
American (AMR)
AF:
AC:
0
AN:
15238
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5178
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10550
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
4
AN:
67960
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.532
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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