10-103345062-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001011663.2(PCGF6):āc.744A>Gā(p.Pro248=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,612,710 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00090 ( 1 hom., cov: 32)
Exomes š: 0.0019 ( 0 hom. )
Consequence
PCGF6
NM_001011663.2 synonymous
NM_001011663.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.524
Genes affected
PCGF6 (HGNC:21156): (polycomb group ring finger 6) The protein encoded by this gene contains a RING finger motif, which is most closely related to those of polycomb group (PcG) proteins RNF110/MEL-18 and BMI1. PcG proteins are known to form protein complexes and function as transcription repressors. This protein has been shown to interact with some PcG proteins and act as a transcription repressor. The activity of this protein is found to be regulated by cell cycle dependent phosphorylation. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 10-103345062-T-C is Benign according to our data. Variant chr10-103345062-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 719987.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.524 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCGF6 | NM_001011663.2 | c.744A>G | p.Pro248= | synonymous_variant | 6/10 | ENST00000369847.4 | NP_001011663.1 | |
PCGF6 | XM_047425832.1 | c.744A>G | p.Pro248= | synonymous_variant | 6/8 | XP_047281788.1 | ||
PCGF6 | XM_047425834.1 | c.*31A>G | 3_prime_UTR_variant | 4/4 | XP_047281790.1 | |||
PCGF6 | NM_032154.4 | c.557+3654A>G | intron_variant | NP_115530.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCGF6 | ENST00000369847.4 | c.744A>G | p.Pro248= | synonymous_variant | 6/10 | 1 | NM_001011663.2 | ENSP00000358862 | P1 | |
PCGF6 | ENST00000337211.8 | c.557+3654A>G | intron_variant | 1 | ENSP00000338845 | |||||
PCGF6 | ENST00000490296.1 | n.781A>G | non_coding_transcript_exon_variant | 6/10 | 2 | |||||
PCGF6 | ENST00000647574.1 | c.*38+2176A>G | intron_variant, NMD_transcript_variant | ENSP00000497672 |
Frequencies
GnomAD3 genomes AF: 0.000900 AC: 137AN: 152162Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000853 AC: 214AN: 250920Hom.: 0 AF XY: 0.000951 AC XY: 129AN XY: 135624
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GnomAD4 exome AF: 0.00189 AC: 2759AN: 1460430Hom.: 0 Cov.: 29 AF XY: 0.00180 AC XY: 1308AN XY: 726570
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GnomAD4 genome AF: 0.000900 AC: 137AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.000846 AC XY: 63AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at