rs918376480

Variant summary

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

The NM_153695.4(ZNF367):​c.334C>T​(p.Pro112Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000197 in 1,015,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. P112T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000020 ( 0 hom. )

Consequence

ZNF367
NM_153695.4 missense

Scores

2
1
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.440
Variant links:
Genes affected
ZNF367 (HGNC:18320): (zinc finger protein 367) Enables DNA-binding transcription factor activity. Acts upstream of or within regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.13177168).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF367NM_153695.4 linkc.334C>T p.Pro112Ser missense_variant Exon 1 of 5 ENST00000375256.5 NP_710162.1 Q7RTV3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF367ENST00000375256.5 linkc.334C>T p.Pro112Ser missense_variant Exon 1 of 5 1 NM_153695.4 ENSP00000364405.4 Q7RTV3-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000197
AC:
2
AN:
1015746
Hom.:
0
Cov.:
19
AF XY:
0.00000416
AC XY:
2
AN XY:
481198
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:
0.0000539
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000115
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
Benign
0.14
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
19
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0096
T
Eigen
Benign
-0.17
Eigen_PC
Benign
-0.10
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.42
T
M_CAP
Pathogenic
0.42
D
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.20
N
PrimateAI
Pathogenic
0.86
D
PROVEAN
Benign
0.46
N
REVEL
Benign
0.041
Sift
Benign
0.039
D
Sift4G
Benign
0.66
T
Polyphen
0.43
B
Vest4
0.18
MutPred
0.30
Gain of phosphorylation at P112 (P = 0.0019);
MVP
0.11
MPC
1.1
ClinPred
0.22
T
GERP RS
2.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.1
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-99179981; API