chr12-132922352-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_183238.4(ZNF605):c.*3021C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,034 control chromosomes in the GnomAD database, including 13,965 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 0.42 ( 13965 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
ZNF605
NM_183238.4 3_prime_UTR
NM_183238.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.559
Publications
11 publications found
Genes affected
ZNF605 (HGNC:28068): (zinc finger protein 605) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
CHFR (HGNC:20455): (checkpoint with forkhead and ring finger domains) This gene encodes an E3 ubiquitin-protein ligase required for the maintenance of the antephase checkpoint that regulates cell cycle entry into mitosis and, therefore, may play a key role in cell cycle progression and tumorigenesis. The encoded protein has an N-terminal forkhead-associated domain, a central RING-finger domain, and a cysteine-rich C-terminal region. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Mar 2014]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF605 | ENST00000360187.9 | c.*3021C>T | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_183238.4 | ENSP00000353314.3 | |||
ZNF605 | ENST00000392321.3 | c.*3021C>T | 3_prime_UTR_variant | Exon 5 of 5 | 2 | ENSP00000376135.3 | ||||
CHFR | ENST00000536932.5 | c.-252+23269C>T | intron_variant | Intron 2 of 5 | 4 | ENSP00000475247.1 |
Frequencies
GnomAD3 genomes AF: 0.416 AC: 63273AN: 151916Hom.: 13966 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
63273
AN:
151916
Hom.:
Cov.:
33
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome AF: 0.416 AC: 63290AN: 152034Hom.: 13965 Cov.: 33 AF XY: 0.412 AC XY: 30644AN XY: 74290 show subpopulations
GnomAD4 genome
AF:
AC:
63290
AN:
152034
Hom.:
Cov.:
33
AF XY:
AC XY:
30644
AN XY:
74290
show subpopulations
African (AFR)
AF:
AC:
12344
AN:
41490
American (AMR)
AF:
AC:
6757
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
1873
AN:
3472
East Asian (EAS)
AF:
AC:
1129
AN:
5162
South Asian (SAS)
AF:
AC:
2545
AN:
4824
European-Finnish (FIN)
AF:
AC:
3788
AN:
10550
Middle Eastern (MID)
AF:
AC:
160
AN:
294
European-Non Finnish (NFE)
AF:
AC:
33165
AN:
67954
Other (OTH)
AF:
AC:
1001
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1860
3720
5580
7440
9300
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
594
1188
1782
2376
2970
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1376
AN:
3478
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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