GeneBe

7-149432385-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_015694.3(ZNF777):​c.1887C>T​(p.Gly629Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000882 in 1,613,232 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00065 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00091 ( 3 hom. )

Consequence

ZNF777
NM_015694.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09
Variant links:
Genes affected
ZNF777 (HGNC:22213): (zinc finger protein 777) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. 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 -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 7-149432385-G-A is Benign according to our data. Variant chr7-149432385-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658143.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.1 with no splicing effect.
BS2
High AC in GnomAd4 at 99 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF777NM_015694.3 linkc.1887C>T p.Gly629Gly synonymous_variant Exon 6 of 6 ENST00000247930.5 NP_056509.2 Q9ULD5
ZNF777XM_005249980.4 linkc.2019C>T p.Gly673Gly synonymous_variant Exon 6 of 6 XP_005250037.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF777ENST00000247930.5 linkc.1887C>T p.Gly629Gly synonymous_variant Exon 6 of 6 1 NM_015694.3 ENSP00000247930.4 Q9ULD5
ENSG00000306674ENST00000820048.1 linkn.433-15218G>A intron_variant Intron 2 of 2
ENSG00000306674ENST00000820049.1 linkn.526-3997G>A intron_variant Intron 2 of 2
ENSG00000306674ENST00000820050.1 linkn.498-3997G>A intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.000657
AC:
100
AN:
152246
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000523
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00118
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.000721
AC:
179
AN:
248158
AF XY:
0.000756
show subpopulations
Gnomad AFR exome
AF:
0.000130
Gnomad AMR exome
AF:
0.000464
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000191
Gnomad NFE exome
AF:
0.00133
Gnomad OTH exome
AF:
0.000828
GnomAD4 exome
AF:
0.000906
AC:
1324
AN:
1460868
Hom.:
3
Cov.:
31
AF XY:
0.000892
AC XY:
648
AN XY:
726824
show subpopulations
African (AFR)
AF:
0.0000896
AC:
3
AN:
33476
American (AMR)
AF:
0.000537
AC:
24
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
0.0000383
AC:
1
AN:
26126
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39696
South Asian (SAS)
AF:
0.0000348
AC:
3
AN:
86258
European-Finnish (FIN)
AF:
0.000248
AC:
13
AN:
52500
Middle Eastern (MID)
AF:
0.00156
AC:
9
AN:
5768
European-Non Finnish (NFE)
AF:
0.00109
AC:
1210
AN:
1111944
Other (OTH)
AF:
0.00101
AC:
61
AN:
60378
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
100
200
301
401
501
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
36
72
108
144
180
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.000650
AC:
99
AN:
152364
Hom.:
0
Cov.:
33
AF XY:
0.000550
AC XY:
41
AN XY:
74516
show subpopulations
African (AFR)
AF:
0.000192
AC:
8
AN:
41596
American (AMR)
AF:
0.000523
AC:
8
AN:
15306
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3466
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5176
South Asian (SAS)
AF:
0.000207
AC:
1
AN:
4832
European-Finnish (FIN)
AF:
0.000188
AC:
2
AN:
10630
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.00118
AC:
80
AN:
68036
Other (OTH)
AF:
0.00
AC:
0
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
5
10
16
21
26
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00121
Hom.:
0
Bravo
AF:
0.000771
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.000763
EpiControl
AF:
0.00107

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Nov 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

ZNF777: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
0.28
DANN
Benign
0.63
PhyloP100
-1.1
Mutation Taster
=96/4
polymorphism

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

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Other links and lift over

dbSNP: rs377235647; hg19: chr7-149129476; COSMIC: COSV56099046; API