1-33489593-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001377376.1(ZSCAN20):c.757G>A(p.Val253Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,613,948 control chromosomes in the GnomAD database, including 2 homozygotes. 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_001377376.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSCAN20 | NM_001377376.1 | c.757G>A | p.Val253Met | missense_variant | 5/8 | ENST00000684572.1 | NP_001364305.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZSCAN20 | ENST00000684572.1 | c.757G>A | p.Val253Met | missense_variant | 5/8 | NM_001377376.1 | ENSP00000507139.1 | |||
ZSCAN20 | ENST00000373413.2 | c.604+942G>A | intron_variant | 1 | ENSP00000362512.1 | |||||
ZSCAN20 | ENST00000361328.7 | c.757G>A | p.Val253Met | missense_variant | 5/8 | 2 | ENSP00000355053.3 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000309 AC: 77AN: 249368Hom.: 1 AF XY: 0.000273 AC XY: 37AN XY: 135302
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461786Hom.: 2 Cov.: 31 AF XY: 0.000164 AC XY: 119AN XY: 727200
GnomAD4 genome AF: 0.000184 AC: 28AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.757G>A (p.V253M) alteration is located in exon 5 (coding exon 4) of the ZSCAN20 gene. This alteration results from a G to A substitution at nucleotide position 757, causing the valine (V) at amino acid position 253 to be replaced by a methionine (M). 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