GeneBe

rs469271

Variant names:

Variant summary

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

The NM_024697.3(ZNF385D):​c.439+28387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,088 control chromosomes in the GnomAD database, including 4,145 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 0.23 ( 4145 hom., cov: 32)

Consequence

ZNF385D
NM_024697.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.591

Publications

2 publications found
Variant links:
Genes affected
ZNF385D (HGNC:26191): (zinc finger protein 385D) Enables sequence-specific double-stranded DNA binding activity. Predicted to be active 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=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF385DNM_024697.3 linkc.439+28387G>A intron_variant Intron 4 of 7 ENST00000281523.8 NP_078973.1 Q9H6B1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF385DENST00000281523.8 linkc.439+28387G>A intron_variant Intron 4 of 7 1 NM_024697.3 ENSP00000281523.2 Q9H6B1

Frequencies

GnomAD3 genomes
AF:
0.231
AC:
35102
AN:
151970
Hom.:
4142
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.193
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.220
Gnomad ASJ
AF:
0.214
Gnomad EAS
AF:
0.276
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.235
Gnomad MID
AF:
0.207
Gnomad NFE
AF:
0.256
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.231
AC:
35129
AN:
152088
Hom.:
4145
Cov.:
32
AF XY:
0.229
AC XY:
17035
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.193
AC:
8001
AN:
41498
American (AMR)
AF:
0.220
AC:
3360
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.214
AC:
743
AN:
3466
East Asian (EAS)
AF:
0.277
AC:
1427
AN:
5148
South Asian (SAS)
AF:
0.199
AC:
958
AN:
4826
European-Finnish (FIN)
AF:
0.235
AC:
2487
AN:
10574
Middle Eastern (MID)
AF:
0.192
AC:
56
AN:
292
European-Non Finnish (NFE)
AF:
0.256
AC:
17407
AN:
67990
Other (OTH)
AF:
0.239
AC:
505
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1391
2782
4172
5563
6954
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
362
724
1086
1448
1810
<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:
0.248
Hom.:
8865
Bravo
AF:
0.228
Asia WGS
AF:
0.230
AC:
799
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.56
DANN
Benign
0.24
PhyloP100
-0.59
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: rs167936; hg19: chr3-21523966; API