rs1056393

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001079906.2(ZNF331):ā€‹c.1185A>Gā€‹(p.Gly395=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 1,614,054 control chromosomes in the GnomAD database, including 5,042 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: š‘“ 0.10 ( 1216 hom., cov: 33)
Exomes š‘“: 0.066 ( 3826 hom. )

Consequence

ZNF331
NM_001079906.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.23
Variant links:
Genes affected
ZNF331 (HGNC:15489): (zinc finger protein 331) This gene encodes a zinc finger protein containing a KRAB (Kruppel-associated box) domain found in transcriptional repressors. This gene may be methylated and silenced in cancer cells. This gene is located within a differentially methylated region (DMR) and shows allele-specific expression in placenta. Alternative splicing and the use of alternative promoters results in multiple transcript variants encoding the same protein. [provided by RefSeq, Nov 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
Synonymous conserved (PhyloP=-4.23 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZNF331NM_001079906.2 linkuse as main transcriptc.1185A>G p.Gly395= synonymous_variant 6/6 ENST00000449416.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZNF331ENST00000449416.6 linkuse as main transcriptc.1185A>G p.Gly395= synonymous_variant 6/65 NM_001079906.2 P1

Frequencies

GnomAD3 genomes
AF:
0.104
AC:
15760
AN:
152066
Hom.:
1217
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.220
Gnomad AMI
AF:
0.0264
Gnomad AMR
AF:
0.0661
Gnomad ASJ
AF:
0.0608
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0180
Gnomad FIN
AF:
0.0531
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0664
Gnomad OTH
AF:
0.104
GnomAD3 exomes
AF:
0.0606
AC:
15235
AN:
251376
Hom.:
746
AF XY:
0.0568
AC XY:
7720
AN XY:
135880
show subpopulations
Gnomad AFR exome
AF:
0.225
Gnomad AMR exome
AF:
0.0383
Gnomad ASJ exome
AF:
0.0675
Gnomad EAS exome
AF:
0.000163
Gnomad SAS exome
AF:
0.0168
Gnomad FIN exome
AF:
0.0555
Gnomad NFE exome
AF:
0.0660
Gnomad OTH exome
AF:
0.0589
GnomAD4 exome
AF:
0.0657
AC:
96009
AN:
1461870
Hom.:
3826
Cov.:
34
AF XY:
0.0634
AC XY:
46097
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.229
Gnomad4 AMR exome
AF:
0.0423
Gnomad4 ASJ exome
AF:
0.0653
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0170
Gnomad4 FIN exome
AF:
0.0523
Gnomad4 NFE exome
AF:
0.0682
Gnomad4 OTH exome
AF:
0.0700
GnomAD4 genome
AF:
0.104
AC:
15778
AN:
152184
Hom.:
1216
Cov.:
33
AF XY:
0.102
AC XY:
7565
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.220
Gnomad4 AMR
AF:
0.0660
Gnomad4 ASJ
AF:
0.0608
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0180
Gnomad4 FIN
AF:
0.0531
Gnomad4 NFE
AF:
0.0664
Gnomad4 OTH
AF:
0.103
Alfa
AF:
0.0738
Hom.:
882
Bravo
AF:
0.110
Asia WGS
AF:
0.0200
AC:
72
AN:
3478
EpiCase
AF:
0.0687
EpiControl
AF:
0.0717

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.68
DANN
Benign
0.60

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: rs1056393; hg19: chr19-54080999; API