12-21527759-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030572.4(SPX):āc.178A>Gā(p.Arg60Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000776 in 1,572,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030572.4 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 |
---|---|---|---|---|---|---|---|
SPX | NM_030572.4 | c.178A>G | p.Arg60Gly | missense_variant | 4/6 | ENST00000256969.7 | |
SPX | NR_135187.2 | n.229A>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPX | ENST00000256969.7 | c.178A>G | p.Arg60Gly | missense_variant | 4/6 | 1 | NM_030572.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000489 AC: 9AN: 184068Hom.: 0 AF XY: 0.0000409 AC XY: 4AN XY: 97770
GnomAD4 exome AF: 0.0000352 AC: 50AN: 1420460Hom.: 0 Cov.: 31 AF XY: 0.0000370 AC XY: 26AN XY: 702158
GnomAD4 genome AF: 0.000473 AC: 72AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | The c.178A>G (p.R60G) alteration is located in exon 4 (coding exon 4) of the SPX gene. This alteration results from a A to G substitution at nucleotide position 178, causing the arginine (R) at amino acid position 60 to be replaced by a glycine (G). 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