rs3734675
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020381.4(PDSS2):āc.7T>Cā(p.Phe3Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00605 in 1,613,980 control chromosomes in the GnomAD database, including 329 homozygotes. 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 Benign (ā ā ).
Frequency
Consequence
NM_020381.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDSS2 | NM_020381.4 | c.7T>C | p.Phe3Leu | missense_variant | 1/8 | ENST00000369037.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDSS2 | ENST00000369037.9 | c.7T>C | p.Phe3Leu | missense_variant | 1/8 | 1 | NM_020381.4 | P1 | |
PDSS2 | ENST00000369031.4 | c.7T>C | p.Phe3Leu | missense_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00880 AC: 1339AN: 152188Hom.: 46 Cov.: 32
GnomAD3 exomes AF: 0.0155 AC: 3895AN: 250590Hom.: 147 AF XY: 0.0144 AC XY: 1957AN XY: 135660
GnomAD4 exome AF: 0.00576 AC: 8414AN: 1461672Hom.: 282 Cov.: 31 AF XY: 0.00571 AC XY: 4152AN XY: 727134
GnomAD4 genome AF: 0.00884 AC: 1347AN: 152308Hom.: 47 Cov.: 32 AF XY: 0.0103 AC XY: 768AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 31, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jun 14, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Kidney disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 24, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at