rs35334289
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000375231.5(ZNF510):c.-604G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,172 control chromosomes in the GnomAD database, including 3,457 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 0.14 ( 3457 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZNF510
ENST00000375231.5 5_prime_UTR
ENST00000375231.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.28
Genes affected
ZNF510 (HGNC:29161): (zinc finger protein 510) This gene encodes a krueppel C2H2-type zinc-finger protein family member. The encoded protein is expressed in several cancer cell types and may be a biomarker for early diagnosis of these cancers. [provided by RefSeq, Sep 2015]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF510 | NM_014930.3 | c.-177+25G>A | intron_variant | ENST00000223428.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF510 | ENST00000375231.5 | c.-604G>A | 5_prime_UTR_variant | 1/6 | 1 | P1 | |||
ZNF510 | ENST00000223428.9 | c.-177+25G>A | intron_variant | 1 | NM_014930.3 | P1 | |||
ZNF510 | ENST00000374641.3 | n.96+25G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.141 AC: 21416AN: 152056Hom.: 3423 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
21416
AN:
152056
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 142Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 104
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
142
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
104
Gnomad4 AMR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.141 AC: 21488AN: 152172Hom.: 3457 Cov.: 32 AF XY: 0.145 AC XY: 10779AN XY: 74376
GnomAD4 genome
?
AF:
AC:
21488
AN:
152172
Hom.:
Cov.:
32
AF XY:
AC XY:
10779
AN XY:
74376
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
671
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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