chr4-7433330-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001085382.2(PSAPL1):c.1550C>T(p.Ala517Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000789 in 1,420,034 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.1550C>T | p.Ala517Val | missense_variant | 1/1 | ENST00000319098.7 | |
SORCS2 | NM_020777.3 | c.548+36975G>A | intron_variant | ENST00000507866.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSAPL1 | ENST00000319098.7 | c.1550C>T | p.Ala517Val | missense_variant | 1/1 | NM_001085382.2 | P1 | ||
SORCS2 | ENST00000507866.6 | c.548+36975G>A | intron_variant | 1 | NM_020777.3 | P1 | |||
SORCS2 | ENST00000511199.1 | n.163+36975G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000434 AC: 66AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000140 AC: 10AN: 71410Hom.: 0 AF XY: 0.0000287 AC XY: 1AN XY: 34870
GnomAD4 exome AF: 0.0000363 AC: 46AN: 1267672Hom.: 0 Cov.: 53 AF XY: 0.0000278 AC XY: 17AN XY: 610788
GnomAD4 genome ? AF: 0.000433 AC: 66AN: 152362Hom.: 0 Cov.: 34 AF XY: 0.000403 AC XY: 30AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.1550C>T (p.A517V) alteration is located in exon 1 (coding exon 1) of the PSAPL1 gene. This alteration results from a C to T substitution at nucleotide position 1550, causing the alanine (A) at amino acid position 517 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