rs749584001

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_020807.3(ZNF319):​c.1264G>C​(p.Gly422Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,453,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. G422S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

ZNF319
NM_020807.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0640
Variant links:
Genes affected
ZNF319 (HGNC:13644): (zinc finger protein 319) Predicted to enable DNA-binding transcription activator 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 by RNA polymerase II. Predicted to be active in nucleus. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11677992).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF319NM_020807.3 linkc.1264G>C p.Gly422Arg missense_variant Exon 2 of 2 ENST00000299237.3 NP_065858.1 Q9P2F9
ZNF319NM_001384365.1 linkc.1264G>C p.Gly422Arg missense_variant Exon 2 of 2 NP_001371294.1
ZNF319NM_001384366.1 linkc.1264G>C p.Gly422Arg missense_variant Exon 3 of 3 NP_001371295.1
ZNF319NM_001384367.1 linkc.1264G>C p.Gly422Arg missense_variant Exon 3 of 3 NP_001371296.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF319ENST00000299237.3 linkc.1264G>C p.Gly422Arg missense_variant Exon 2 of 2 1 NM_020807.3 ENSP00000299237.2 Q9P2F9

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1453174
Hom.:
0
Cov.:
34
AF XY:
0.00000138
AC XY:
1
AN XY:
722682
show subpopulations
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:
9.01e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.34
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
9.7
DANN
Benign
0.88
DEOGEN2
Benign
0.027
T
Eigen
Benign
-1.0
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.12
N
LIST_S2
Benign
0.76
T
M_CAP
Benign
0.021
T
MetaRNN
Benign
0.12
T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.42
N
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
0.56
N
REVEL
Benign
0.069
Sift
Benign
0.085
T
Sift4G
Benign
0.14
T
Polyphen
0.75
P
Vest4
0.29
MutPred
0.54
Gain of MoRF binding (P = 0.0341);
MVP
0.043
MPC
1.7
ClinPred
0.094
T
GERP RS
-0.96
Varity_R
0.035
gMVP
0.30

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: rs749584001; hg19: chr16-58030906; API