rs778876349

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_178457.3(ZNF831):​c.194C>A​(p.Thr65Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T65M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ZNF831
NM_178457.3 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14
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 made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30144882).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF831NM_178457.3 linkc.194C>A p.Thr65Lys missense_variant Exon 2 of 6 ENST00000371030.4 NP_848552.1 Q5JPB2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF831ENST00000371030.4 linkc.194C>A p.Thr65Lys missense_variant Exon 2 of 6 1 NM_178457.3 ENSP00000360069.2 Q5JPB2
ZNF831ENST00000637017.1 linkc.194C>A p.Thr65Lys missense_variant Exon 4 of 8 5 ENSP00000490240.1 Q5JPB2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1412090
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
698244
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.42
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.097
T;T
Eigen
Benign
0.045
Eigen_PC
Benign
0.052
FATHMM_MKL
Benign
0.73
D
LIST_S2
Benign
0.76
.;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.30
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.2
M;M
PrimateAI
Uncertain
0.49
T
PROVEAN
Uncertain
-2.9
.;D
REVEL
Benign
0.16
Sift
Uncertain
0.0080
.;D
Sift4G
Benign
0.14
.;T
Polyphen
1.0
D;D
Vest4
0.38
MutPred
0.41
Gain of methylation at T65 (P = 0.0122);Gain of methylation at T65 (P = 0.0122);
MVP
0.081
MPC
0.88
ClinPred
0.96
D
GERP RS
4.7
Varity_R
0.19
gMVP
0.42

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-57766268; API