chrX-47412539-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003446.4(ZNF157):c.466C>T(p.Pro156Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,210,357 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003446.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112147Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34335
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183247Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67761
GnomAD4 exome AF: 0.0000401 AC: 44AN: 1098210Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 15AN XY: 363570
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112147Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34335
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.466C>T (p.P156S) alteration is located in exon 4 (coding exon 4) of the ZNF157 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the proline (P) at amino acid position 156 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at