chr4-7433502-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001085382.2(PSAPL1):c.1378G>A(p.Val460Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,601,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001085382.2 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 |
---|---|---|---|---|---|---|---|
PSAPL1 | NM_001085382.2 | c.1378G>A | p.Val460Met | missense_variant | 1/1 | ENST00000319098.7 | |
SORCS2 | NM_020777.3 | c.548+37147C>T | intron_variant | ENST00000507866.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSAPL1 | ENST00000319098.7 | c.1378G>A | p.Val460Met | missense_variant | 1/1 | NM_001085382.2 | P1 | ||
SORCS2 | ENST00000507866.6 | c.548+37147C>T | intron_variant | 1 | NM_020777.3 | P1 | |||
SORCS2 | ENST00000511199.1 | n.163+37147C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000390 AC: 9AN: 230646Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125314
GnomAD4 exome AF: 0.0000179 AC: 26AN: 1449472Hom.: 0 Cov.: 63 AF XY: 0.0000125 AC XY: 9AN XY: 720086
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.1378G>A (p.V460M) alteration is located in exon 1 (coding exon 1) of the PSAPL1 gene. This alteration results from a G to A substitution at nucleotide position 1378, causing the valine (V) at amino acid position 460 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