Menu
GeneBe

19-22391897-T-G

Variant summary

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

The NM_001098626.2(ZNF98):c.1338A>C(p.Ser446=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000604 in 1,126,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00046 ( 0 hom., cov: 12)
Exomes 𝑓: 0.00060 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ZNF98
NM_001098626.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.66
Variant links:
Genes affected
ZNF98 (HGNC:13174): (zinc finger protein 98) 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, DNA-templated. Predicted to be located 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
Computational evidence support a benign effect (BayesDel_noAF=-1.09).
BP6
Variant 19-22391897-T-G is Benign according to our data. Variant chr19-22391897-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2649650.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.66 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF98NM_001098626.2 linkuse as main transcriptc.1338A>C p.Ser446= synonymous_variant 4/4 ENST00000357774.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF98ENST00000357774.9 linkuse as main transcriptc.1338A>C p.Ser446= synonymous_variant 4/41 NM_001098626.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
33
AN:
72248
Hom.:
0
Cov.:
12
FAILED QC
Gnomad AFR
AF:
0.000978
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000434
Gnomad ASJ
AF:
0.000645
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000283
Gnomad OTH
AF:
0.00107
GnomAD3 exomes
AF:
0.0000872
AC:
15
AN:
171942
Hom.:
0
AF XY:
0.0000539
AC XY:
5
AN XY:
92728
show subpopulations
Gnomad AFR exome
AF:
0.000103
Gnomad AMR exome
AF:
0.000157
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000339
Gnomad SAS exome
AF:
0.000334
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000604
AC:
681
AN:
1126726
Hom.:
0
Cov.:
33
AF XY:
0.000684
AC XY:
383
AN XY:
559872
show subpopulations
Gnomad4 AFR exome
AF:
0.00107
Gnomad4 AMR exome
AF:
0.00287
Gnomad4 ASJ exome
AF:
0.000771
Gnomad4 EAS exome
AF:
0.00244
Gnomad4 SAS exome
AF:
0.00269
Gnomad4 FIN exome
AF:
0.000325
Gnomad4 NFE exome
AF:
0.000269
Gnomad4 OTH exome
AF:
0.00112
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000456
AC:
33
AN:
72310
Hom.:
0
Cov.:
12
AF XY:
0.000494
AC XY:
17
AN XY:
34398
show subpopulations
Gnomad4 AFR
AF:
0.000974
Gnomad4 AMR
AF:
0.000433
Gnomad4 ASJ
AF:
0.000645
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000283
Gnomad4 OTH
AF:
0.00105

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 TuebingenAug 01, 2023ZNF98: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
Cadd
Benign
2.3
Dann
Benign
0.21

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: rs4100185; hg19: chr19-22574699; API