rs194869

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_178457.3(ZNF831):​c.3738+150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000001 in 995,512 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000010 ( 0 hom. )

Consequence

ZNF831
NM_178457.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.33

Publications

0 publications found
Variant links:
Genes affected
ZNF831 (HGNC:16167): (zinc finger protein 831) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF831NM_178457.3 linkc.3738+150C>A intron_variant Intron 2 of 5 ENST00000371030.4 NP_848552.1 Q5JPB2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF831ENST00000371030.4 linkc.3738+150C>A intron_variant Intron 2 of 5 1 NM_178457.3 ENSP00000360069.2 Q5JPB2
ZNF831ENST00000637017.1 linkc.3738+150C>A intron_variant Intron 4 of 7 5 ENSP00000490240.1 Q5JPB2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000100
AC:
1
AN:
995512
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
484260
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
22256
American (AMR)
AF:
0.00
AC:
0
AN:
13594
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16042
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30978
South Asian (SAS)
AF:
0.00
AC:
0
AN:
40340
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40936
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2916
European-Non Finnish (NFE)
AF:
0.00000127
AC:
1
AN:
785876
Other (OTH)
AF:
0.00
AC:
0
AN:
42574
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.084
DANN
Benign
0.46
PhyloP100
-2.3

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

Other links and lift over

dbSNP: rs194869; hg19: chr20-57769962; API