Menu
GeneBe

20-45948675-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_022095.4(ZNF335):c.*278G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 448,752 control chromosomes in the GnomAD database, including 5,988 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2514 hom., cov: 33)
Exomes 𝑓: 0.14 ( 3474 hom. )

Consequence

ZNF335
NM_022095.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.441
Variant links:
Genes affected
ZNF335 (HGNC:15807): (zinc finger protein 335) The protein encoded by this gene enhances transcriptional activation by ligand-bound nuclear hormone receptors. However, it does this not by direct interaction with the receptor, but by direct interaction with the nuclear hormone receptor transcriptional coactivator NRC. The encoded protein may function by altering local chromatin structure. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 20-45948675-C-T is Benign according to our data. Variant chr20-45948675-C-T is described in ClinVar as [Benign]. Clinvar id is 1231704.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF335NM_022095.4 linkuse as main transcriptc.*278G>A 3_prime_UTR_variant 28/28 ENST00000322927.3
ZNF335XM_005260504.5 linkuse as main transcriptc.*278G>A 3_prime_UTR_variant 27/27
ZNF335XM_047440363.1 linkuse as main transcriptc.*278G>A 3_prime_UTR_variant 27/27

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF335ENST00000322927.3 linkuse as main transcriptc.*278G>A 3_prime_UTR_variant 28/281 NM_022095.4 P1Q9H4Z2-1

Frequencies

GnomAD3 genomes
AF:
0.166
AC:
25179
AN:
152042
Hom.:
2511
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.273
Gnomad AMI
AF:
0.0877
Gnomad AMR
AF:
0.0961
Gnomad ASJ
AF:
0.109
Gnomad EAS
AF:
0.324
Gnomad SAS
AF:
0.188
Gnomad FIN
AF:
0.125
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.114
Gnomad OTH
AF:
0.142
GnomAD4 exome
AF:
0.137
AC:
40618
AN:
296590
Hom.:
3474
Cov.:
3
AF XY:
0.140
AC XY:
22109
AN XY:
157834
show subpopulations
Gnomad4 AFR exome
AF:
0.265
Gnomad4 AMR exome
AF:
0.0944
Gnomad4 ASJ exome
AF:
0.106
Gnomad4 EAS exome
AF:
0.315
Gnomad4 SAS exome
AF:
0.176
Gnomad4 FIN exome
AF:
0.111
Gnomad4 NFE exome
AF:
0.112
Gnomad4 OTH exome
AF:
0.129
GnomAD4 genome
AF:
0.166
AC:
25202
AN:
152162
Hom.:
2514
Cov.:
33
AF XY:
0.167
AC XY:
12409
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.273
Gnomad4 AMR
AF:
0.0962
Gnomad4 ASJ
AF:
0.109
Gnomad4 EAS
AF:
0.325
Gnomad4 SAS
AF:
0.187
Gnomad4 FIN
AF:
0.125
Gnomad4 NFE
AF:
0.114
Gnomad4 OTH
AF:
0.139
Alfa
AF:
0.115
Hom.:
1845
Bravo
AF:
0.169

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 27, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
Cadd
Benign
6.4
Dann
Benign
0.62
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3363; hg19: chr20-44577314; API