chr6-30604080-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002714.4(PPP1R10):āc.1436A>Gā(p.Asn479Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,461,848 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 (ā ).
Frequency
Consequence
NM_002714.4 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 | UniProt |
---|---|---|---|---|---|---|---|
PPP1R10 | NM_002714.4 | c.1436A>G | p.Asn479Ser | missense_variant | 14/20 | ENST00000376511.7 | |
PPP1R10 | NM_001376195.1 | c.1436A>G | p.Asn479Ser | missense_variant | 14/20 | ||
PPP1R10 | XM_011514722.2 | c.1436A>G | p.Asn479Ser | missense_variant | 15/21 | ||
PPP1R10 | NR_072994.2 | n.1927A>G | non_coding_transcript_exon_variant | 14/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R10 | ENST00000376511.7 | c.1436A>G | p.Asn479Ser | missense_variant | 14/20 | 1 | NM_002714.4 | P1 | |
PPP1R10 | ENST00000496955.1 | n.133A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251134Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135726
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461848Hom.: 0 Cov.: 33 AF XY: 0.0000289 AC XY: 21AN XY: 727228
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.1436A>G (p.N479S) alteration is located in exon 14 (coding exon 12) of the PPP1R10 gene. This alteration results from a A to G substitution at nucleotide position 1436, causing the asparagine (N) at amino acid position 479 to be replaced by a serine (S). 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