19-58338340-C-T

Variant summary

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

The NM_181846.3(ZSCAN22):​c.490C>T​(p.Leu164Phe) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

ZSCAN22
NM_181846.3 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0220
Variant links:
Genes affected
ZSCAN22 (HGNC:4929): (zinc finger and SCAN domain containing 22) Predicted to enable DNA-binding transcription factor 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 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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.075380385).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZSCAN22NM_181846.3 linkc.490C>T p.Leu164Phe missense_variant Exon 3 of 3 ENST00000329665.5 NP_862829.1 P10073

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZSCAN22ENST00000329665.5 linkc.490C>T p.Leu164Phe missense_variant Exon 3 of 3 1 NM_181846.3 ENSP00000332433.3 P10073

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jul 30, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.490C>T (p.L164F) alteration is located in exon 3 (coding exon 2) of the ZSCAN22 gene. This alteration results from a C to T substitution at nucleotide position 490, causing the leucine (L) at amino acid position 164 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.36
T
BayesDel_noAF
Benign
-0.76
CADD
Benign
2.4
DANN
Uncertain
0.99
DEOGEN2
Benign
0.037
T
Eigen
Benign
-0.93
Eigen_PC
Benign
-0.92
FATHMM_MKL
Benign
0.0078
N
LIST_S2
Benign
0.41
T
M_CAP
Benign
0.0035
T
MetaRNN
Benign
0.075
T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
0.55
N
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.019
Sift
Benign
0.067
T
Sift4G
Benign
0.062
T
Polyphen
0.12
B
Vest4
0.013
MutPred
0.21
Gain of catalytic residue at L164 (P = 0.0179);
MVP
0.081
MPC
0.12
ClinPred
0.081
T
GERP RS
0.50
Varity_R
0.057
gMVP
0.086

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: chr19-58849706; API