chr7-100057398-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000292450.9(ZSCAN21):āc.392G>Cā(p.Gly131Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000647 in 1,546,454 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G131R) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000292450.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSCAN21 | NM_145914.3 | c.392G>C | p.Gly131Ala | missense_variant | 2/4 | ENST00000292450.9 | NP_666019.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZSCAN21 | ENST00000292450.9 | c.392G>C | p.Gly131Ala | missense_variant | 2/4 | 1 | NM_145914.3 | ENSP00000292450.4 | ||
ZSCAN21 | ENST00000456748.6 | c.392G>C | p.Gly131Ala | missense_variant | 2/5 | 5 | ENSP00000390960.2 | |||
ZSCAN21 | ENST00000438937.1 | c.392G>C | p.Gly131Ala | missense_variant | 3/4 | 2 | ENSP00000404207.1 | |||
ZSCAN21 | ENST00000477297.1 | n.488G>C | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000216 AC: 4AN: 185098Hom.: 0 AF XY: 0.0000404 AC XY: 4AN XY: 99086
GnomAD4 exome AF: 0.00000574 AC: 8AN: 1394224Hom.: 0 Cov.: 31 AF XY: 0.00000582 AC XY: 4AN XY: 687070
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2024 | The c.392G>C (p.G131A) alteration is located in exon 2 (coding exon 1) of the ZSCAN21 gene. This alteration results from a G to C substitution at nucleotide position 392, causing the glycine (G) at amino acid position 131 to be replaced by an alanine (A). 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