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GeneBe

19-53238190-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_182609.4(ZNF677):c.537C>T(p.Ala179=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,613,374 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 6 hom. )

Consequence

ZNF677
NM_182609.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.59
Variant links:
Genes affected
ZNF677 (HGNC:28730): (zinc finger protein 677) 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 made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-53238190-G-A is Benign according to our data. Variant chr19-53238190-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650407.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.6 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF677NM_182609.4 linkuse as main transcriptc.537C>T p.Ala179= synonymous_variant 5/5 ENST00000598513.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF677ENST00000598513.6 linkuse as main transcriptc.537C>T p.Ala179= synonymous_variant 5/51 NM_182609.4 P1
ZNF677ENST00000333952.8 linkuse as main transcriptc.537C>T p.Ala179= synonymous_variant 3/32 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00140
AC:
213
AN:
151958
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000363
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000459
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00167
Gnomad FIN
AF:
0.00123
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00240
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.00111
AC:
278
AN:
250546
Hom.:
1
AF XY:
0.00114
AC XY:
155
AN XY:
135464
show subpopulations
Gnomad AFR exome
AF:
0.000247
Gnomad AMR exome
AF:
0.000348
Gnomad ASJ exome
AF:
0.000597
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000886
Gnomad FIN exome
AF:
0.00144
Gnomad NFE exome
AF:
0.00169
Gnomad OTH exome
AF:
0.00115
GnomAD4 exome
AF:
0.00105
AC:
1528
AN:
1461298
Hom.:
6
Cov.:
33
AF XY:
0.00109
AC XY:
793
AN XY:
726900
show subpopulations
Gnomad4 AFR exome
AF:
0.000359
Gnomad4 AMR exome
AF:
0.000358
Gnomad4 ASJ exome
AF:
0.000498
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000685
Gnomad4 FIN exome
AF:
0.00133
Gnomad4 NFE exome
AF:
0.00114
Gnomad4 OTH exome
AF:
0.000795
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00140
AC:
213
AN:
152076
Hom.:
0
Cov.:
33
AF XY:
0.00128
AC XY:
95
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.000362
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00167
Gnomad4 FIN
AF:
0.00123
Gnomad4 NFE
AF:
0.00240
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00221
Hom.:
2
Bravo
AF:
0.000910
EpiCase
AF:
0.00136
EpiControl
AF:
0.00119

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023ZNF677: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
4.6
Dann
Benign
0.25

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144707444; hg19: chr19-53741443; API