chr1-109659072-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000850.5(GSTM4):c.529G>T(p.Ala177Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Consequence
NM_000850.5 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 | UniProt |
---|---|---|---|---|---|---|---|
GSTM4 | NM_000850.5 | c.529G>T | p.Ala177Ser | missense_variant | 7/8 | ENST00000369836.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSTM4 | ENST00000369836.9 | c.529G>T | p.Ala177Ser | missense_variant | 7/8 | 1 | NM_000850.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000755 AC: 19AN: 251494Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135920
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461892Hom.: 0 Cov.: 60 AF XY: 0.0000275 AC XY: 20AN XY: 727246
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.529G>T (p.A177S) alteration is located in exon 7 (coding exon 7) of the GSTM4 gene. This alteration results from a G to T substitution at nucleotide position 529, causing the alanine (A) at amino acid position 177 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