6-30602601-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000376511.7(PPP1R10):c.2048C>T(p.Pro683Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,575,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000376511.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R10 | NM_002714.4 | c.2048C>T | p.Pro683Leu | missense_variant | 19/20 | ENST00000376511.7 | NP_002705.2 | |
PPP1R10 | NM_001376195.1 | c.2048C>T | p.Pro683Leu | missense_variant | 19/20 | NP_001363124.1 | ||
PPP1R10 | XM_011514722.2 | c.2048C>T | p.Pro683Leu | missense_variant | 20/21 | XP_011513024.1 | ||
PPP1R10 | NR_072994.2 | n.2539C>T | non_coding_transcript_exon_variant | 19/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R10 | ENST00000376511.7 | c.2048C>T | p.Pro683Leu | missense_variant | 19/20 | 1 | NM_002714.4 | ENSP00000365694 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000534 AC: 8AN: 149908Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 8AN: 200624Hom.: 0 AF XY: 0.0000271 AC XY: 3AN XY: 110606
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1425338Hom.: 0 Cov.: 32 AF XY: 0.00000566 AC XY: 4AN XY: 706954
GnomAD4 genome AF: 0.0000534 AC: 8AN: 149908Hom.: 0 Cov.: 32 AF XY: 0.0000683 AC XY: 5AN XY: 73206
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.2048C>T (p.P683L) alteration is located in exon 19 (coding exon 17) of the PPP1R10 gene. This alteration results from a C to T substitution at nucleotide position 2048, causing the proline (P) at amino acid position 683 to be replaced by a leucine (L). 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