5-139813658-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032289.4(PSD2):āc.721A>Gā(p.Met241Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032289.4 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 |
---|---|---|---|---|---|---|---|
PSD2 | NM_032289.4 | c.721A>G | p.Met241Val | missense_variant | 3/15 | ENST00000274710.4 | |
PSD2 | XM_017009976.2 | c.721A>G | p.Met241Val | missense_variant | 4/16 | ||
PSD2 | XM_017009977.2 | c.721A>G | p.Met241Val | missense_variant | 4/16 | ||
PSD2 | XM_047417829.1 | c.721A>G | p.Met241Val | missense_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSD2 | ENST00000274710.4 | c.721A>G | p.Met241Val | missense_variant | 3/15 | 1 | NM_032289.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000612 AC: 15AN: 244902Hom.: 0 AF XY: 0.0000749 AC XY: 10AN XY: 133466
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461534Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727072
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152332Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.721A>G (p.M241V) alteration is located in exon 3 (coding exon 2) of the PSD2 gene. This alteration results from a A to G substitution at nucleotide position 721, causing the methionine (M) at amino acid position 241 to be replaced by a valine (V). 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