rs1133146
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024733.5(ZNF665):c.*1046C>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 0.516 in 152,062 control chromosomes in the GnomAD database, including 22,956 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 0.52 ( 22954 hom., cov: 32)
Exomes 𝑓: 0.67 ( 2 hom. )
Consequence
ZNF665
NM_024733.5 3_prime_UTR
NM_024733.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
Publications
6 publications found
Genes affected
ZNF665 (HGNC:25885): (zinc finger protein 665) 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]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF665 | ENST00000396424.5 | c.*1046C>T | 3_prime_UTR_variant | Exon 4 of 4 | 2 | NM_024733.5 | ENSP00000379702.2 | |||
ENSG00000268842 | ENST00000600257.1 | n.203G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
ZNF665 | ENST00000596564.1 | n.50+443C>T | intron_variant | Intron 1 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78459AN: 151940Hom.: 22942 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
78459
AN:
151940
Hom.:
Cov.:
32
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 AF: 0.667 AC: 4AN: 6Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4AN XY: 6 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
6
Hom.:
Cov.:
0
AF XY:
AC XY:
4
AN XY:
6
show subpopulations
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)
AF:
AC:
4
AN:
4
Other (OTH)
AF:
AC:
0
AN:
2
GnomAD4 genome AF: 0.516 AC: 78500AN: 152056Hom.: 22954 Cov.: 32 AF XY: 0.524 AC XY: 38951AN XY: 74294 show subpopulations
GnomAD4 genome
AF:
AC:
78500
AN:
152056
Hom.:
Cov.:
32
AF XY:
AC XY:
38951
AN XY:
74294
show subpopulations
African (AFR)
AF:
AC:
9510
AN:
41500
American (AMR)
AF:
AC:
9415
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1758
AN:
3466
East Asian (EAS)
AF:
AC:
3382
AN:
5154
South Asian (SAS)
AF:
AC:
3448
AN:
4816
European-Finnish (FIN)
AF:
AC:
7044
AN:
10552
Middle Eastern (MID)
AF:
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
AC:
42141
AN:
67976
Other (OTH)
AF:
AC:
1094
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1705
3411
5116
6822
8527
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2268
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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