GeneBe

NM_152520.6:c.299-82936T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152520.6(ZNF385B):​c.299-82936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,098 control chromosomes in the GnomAD database, including 1,951 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 0.15 ( 1951 hom., cov: 32)

Consequence

ZNF385B
NM_152520.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

6 publications found
Variant links:
Genes affected
ZNF385B (HGNC:26332): (zinc finger protein 385B) Enables p53 binding activity. Involved in intrinsic apoptotic signaling pathway by p53 class mediator. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF385BNM_152520.6 linkc.299-82936T>C intron_variant Intron 3 of 9 ENST00000410066.7 NP_689733.4 Q569K4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF385BENST00000410066.7 linkc.299-82936T>C intron_variant Intron 3 of 9 1 NM_152520.6 ENSP00000386845.2 A0A2U3TZT0

Frequencies

GnomAD3 genomes
AF:
0.154
AC:
23411
AN:
151980
Hom.:
1948
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.126
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.232
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.249
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.146
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.165
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.154
AC:
23433
AN:
152098
Hom.:
1951
Cov.:
32
AF XY:
0.156
AC XY:
11617
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.126
AC:
5233
AN:
41510
American (AMR)
AF:
0.232
AC:
3543
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.198
AC:
686
AN:
3472
East Asian (EAS)
AF:
0.249
AC:
1284
AN:
5160
South Asian (SAS)
AF:
0.155
AC:
745
AN:
4816
European-Finnish (FIN)
AF:
0.146
AC:
1547
AN:
10580
Middle Eastern (MID)
AF:
0.241
AC:
71
AN:
294
European-Non Finnish (NFE)
AF:
0.146
AC:
9913
AN:
67980
Other (OTH)
AF:
0.164
AC:
347
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1001
2002
3003
4004
5005
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
254
508
762
1016
1270
<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:
0.156
Hom.:
3258
Bravo
AF:
0.162
Asia WGS
AF:
0.218
AC:
754
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.3
DANN
Benign
0.62
PhyloP100
0.082
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs1515274; hg19: chr2-180492632; API