GeneBe

chr3-21474213-C-T

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+36648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 151,638 control chromosomes in the GnomAD database, including 5,515 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 0.26 ( 5515 hom., cov: 31)

Consequence

ZNF385D
NM_024697.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.795

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF385DNM_024697.3 linkc.439+36648G>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+36648G>A intron_variant Intron 4 of 7 1 NM_024697.3 ENSP00000281523.2 Q9H6B1

Frequencies

GnomAD3 genomes
AF:
0.257
AC:
38975
AN:
151520
Hom.:
5502
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.243
Gnomad ASJ
AF:
0.345
Gnomad EAS
AF:
0.112
Gnomad SAS
AF:
0.199
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.257
AC:
39036
AN:
151638
Hom.:
5515
Cov.:
31
AF XY:
0.257
AC XY:
19035
AN XY:
74052
show subpopulations
African (AFR)
AF:
0.365
AC:
15090
AN:
41330
American (AMR)
AF:
0.244
AC:
3704
AN:
15200
Ashkenazi Jewish (ASJ)
AF:
0.345
AC:
1194
AN:
3462
East Asian (EAS)
AF:
0.112
AC:
577
AN:
5156
South Asian (SAS)
AF:
0.199
AC:
950
AN:
4782
European-Finnish (FIN)
AF:
0.239
AC:
2508
AN:
10506
Middle Eastern (MID)
AF:
0.361
AC:
106
AN:
294
European-Non Finnish (NFE)
AF:
0.206
AC:
13952
AN:
67892
Other (OTH)
AF:
0.271
AC:
571
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1412
2824
4237
5649
7061
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
398
796
1194
1592
1990
<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:
0.228
Hom.:
6981
Bravo
AF:
0.264
Asia WGS
AF:
0.197
AC:
685
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.63
DANN
Benign
0.38
PhyloP100
-0.80
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: rs3860575; hg19: chr3-21515705; API