chr6-42989654-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_006245.4(PPP2R5D):c.71C>T(p.Ser24Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S24S) has been classified as Likely benign.
Frequency
Consequence
NM_006245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP2R5D | NM_006245.4 | c.71C>T | p.Ser24Leu | missense_variant | 2/16 | ENST00000485511.6 | |
PPP2R5D | NM_180976.3 | c.71C>T | p.Ser24Leu | missense_variant | 2/16 | ||
PPP2R5D | NM_001270476.2 | c.-400C>T | 5_prime_UTR_variant | 2/16 | |||
PPP2R5D | NM_180977.3 | c.27+4950C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP2R5D | ENST00000485511.6 | c.71C>T | p.Ser24Leu | missense_variant | 2/16 | 1 | NM_006245.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250906Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135714
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461640Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727118
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at