rs78797427

Variant summary

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

The NM_024833.3(ZNF671):​c.1208G>C​(p.Gly403Ala) 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. G403E) has been classified as Benign.

Frequency

Genomes: not found (cov: 33)

Consequence

ZNF671
NM_024833.3 missense

Scores

2
4
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.769
Variant links:
Genes affected
ZNF671 (HGNC:26279): (zinc finger protein 671) Predicted to enable DNA-binding transcription factor activity 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.38081664).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF671NM_024833.3 linkc.1208G>C p.Gly403Ala missense_variant Exon 4 of 4 ENST00000317398.10 NP_079109.2 Q8TAW3
ZNF671NM_001321376.2 linkc.977G>C p.Gly326Ala missense_variant Exon 5 of 5 NP_001308305.1
ZNF671NM_001321375.2 linkc.914G>C p.Gly305Ala missense_variant Exon 3 of 3 NP_001308304.1 B7Z1N1
ZNF671XM_017027314.2 linkc.977G>C p.Gly326Ala missense_variant Exon 4 of 4 XP_016882803.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF671ENST00000317398.10 linkc.1208G>C p.Gly403Ala missense_variant Exon 4 of 4 1 NM_024833.3 ENSP00000321848.5 Q8TAW3
ENSG00000269026ENST00000594684.1 linkc.34-29907C>G intron_variant Intron 1 of 2 1 ENSP00000472160.1 M0R1X1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.63
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
20
DANN
Uncertain
1.0
DEOGEN2
Benign
0.25
T
Eigen
Benign
-0.090
Eigen_PC
Benign
-0.37
FATHMM_MKL
Benign
0.42
N
LIST_S2
Benign
0.77
T
M_CAP
Benign
0.0051
T
MetaRNN
Benign
0.38
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.1
M
PrimateAI
Benign
0.45
T
PROVEAN
Pathogenic
-5.7
D
REVEL
Benign
0.036
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.0050
D
Polyphen
1.0
D
Vest4
0.20
MutPred
0.69
Loss of ubiquitination at K404 (P = 0.0896);
MVP
0.55
MPC
0.68
ClinPred
0.97
D
GERP RS
0.81
Varity_R
0.47
gMVP
0.082

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: rs78797427; hg19: chr19-58232246; API