chr9-37331608-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032226.3(ZCCHC7):c.987+3774T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,582 control chromosomes in the GnomAD database, including 1,747 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 0.14 ( 1747 hom., cov: 32)
Consequence
ZCCHC7
NM_032226.3 intron
NM_032226.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.328
Publications
2 publications found
Genes affected
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.141 AC: 21317AN: 151464Hom.: 1745 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21317
AN:
151464
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.141 AC: 21317AN: 151582Hom.: 1747 Cov.: 32 AF XY: 0.144 AC XY: 10657AN XY: 74062 show subpopulations
GnomAD4 genome
AF:
AC:
21317
AN:
151582
Hom.:
Cov.:
32
AF XY:
AC XY:
10657
AN XY:
74062
show subpopulations
African (AFR)
AF:
AC:
2946
AN:
41484
American (AMR)
AF:
AC:
2263
AN:
15194
Ashkenazi Jewish (ASJ)
AF:
AC:
415
AN:
3462
East Asian (EAS)
AF:
AC:
515
AN:
5160
South Asian (SAS)
AF:
AC:
652
AN:
4816
European-Finnish (FIN)
AF:
AC:
2578
AN:
10580
Middle Eastern (MID)
AF:
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
AC:
11516
AN:
67574
Other (OTH)
AF:
AC:
289
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
919
1839
2758
3678
4597
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
234
468
702
936
1170
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
484
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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