20-3824277-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018347.3(AP5S1):āc.583A>Gā(p.Ser195Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,526 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_018347.3 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 |
---|---|---|---|---|---|---|---|
AP5S1 | NM_018347.3 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 | ENST00000615891.2 | |
AP5S1 | NM_001204446.2 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 | ||
AP5S1 | NM_001204447.2 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5S1 | ENST00000615891.2 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 | 1 | NM_018347.3 | P1 | |
AP5S1 | ENST00000379573.6 | c.*399A>G | 3_prime_UTR_variant | 3/3 | 1 | ||||
AP5S1 | ENST00000246041.6 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 | 4 | P1 | ||
AP5S1 | ENST00000379567.6 | c.583A>G | p.Ser195Gly | missense_variant | 3/3 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 250952Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135652
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461148Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726758
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152378Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.583A>G (p.S195G) alteration is located in exon 3 (coding exon 2) of the AP5S1 gene. This alteration results from a A to G substitution at nucleotide position 583, causing the serine (S) at amino acid position 195 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