GeneBe

NM_024697.3:c.277-25581A>G

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.277-25581A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,192 control chromosomes in the GnomAD database, including 70,764 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 0.96 ( 70764 hom., cov: 32)

Consequence

ZNF385D
NM_024697.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.756

Publications

1 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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF385DNM_024697.3 linkc.277-25581A>G intron_variant Intron 3 of 7 ENST00000281523.8 NP_078973.1 Q9H6B1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF385DENST00000281523.8 linkc.277-25581A>G intron_variant Intron 3 of 7 1 NM_024697.3 ENSP00000281523.2 Q9H6B1

Frequencies

GnomAD3 genomes
AF:
0.964
AC:
146587
AN:
152074
Hom.:
70700
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.990
Gnomad AMI
AF:
0.946
Gnomad AMR
AF:
0.963
Gnomad ASJ
AF:
0.896
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.997
Gnomad FIN
AF:
0.964
Gnomad MID
AF:
0.927
Gnomad NFE
AF:
0.947
Gnomad OTH
AF:
0.961
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.964
AC:
146710
AN:
152192
Hom.:
70764
Cov.:
32
AF XY:
0.964
AC XY:
71744
AN XY:
74386
show subpopulations
African (AFR)
AF:
0.990
AC:
41142
AN:
41558
American (AMR)
AF:
0.963
AC:
14723
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.896
AC:
3110
AN:
3472
East Asian (EAS)
AF:
1.00
AC:
5174
AN:
5174
South Asian (SAS)
AF:
0.997
AC:
4705
AN:
4720
European-Finnish (FIN)
AF:
0.964
AC:
10235
AN:
10616
Middle Eastern (MID)
AF:
0.925
AC:
272
AN:
294
European-Non Finnish (NFE)
AF:
0.947
AC:
64453
AN:
68038
Other (OTH)
AF:
0.962
AC:
2033
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
274
547
821
1094
1368
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<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:
0.949
Hom.:
33209
Bravo
AF:
0.965
Asia WGS
AF:
0.994
AC:
3454
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.65
DANN
Benign
0.64
PhyloP100
-0.76
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: rs161196; hg19: chr3-21578096; API