chr20-41166245-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002660.3(PLCG1):c.1851G>A(p.Gly617=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,614,144 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0081 ( 7 hom., cov: 32)
Exomes 𝑓: 0.011 ( 106 hom. )
Consequence
PLCG1
NM_002660.3 synonymous
NM_002660.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.949
Genes affected
PLCG1 (HGNC:9065): (phospholipase C gamma 1) The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of receptor-mediated tyrosine kinase activators. For example, when activated by SRC, the encoded protein causes the Ras guanine nucleotide exchange factor RasGRP1 to translocate to the Golgi, where it activates Ras. Also, this protein has been shown to be a major substrate for heparin-binding growth factor 1 (acidic fibroblast growth factor)-activated tyrosine kinase. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 20-41166245-G-A is Benign according to our data. Variant chr20-41166245-G-A is described in ClinVar as [Benign]. Clinvar id is 789125.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.949 with no splicing effect.
BS2
?
High AC in GnomAd at 1229 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCG1 | NM_002660.3 | c.1851G>A | p.Gly617= | synonymous_variant | 17/32 | ENST00000685551.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCG1 | ENST00000685551.1 | c.1851G>A | p.Gly617= | synonymous_variant | 17/32 | NM_002660.3 | P3 | ||
PLCG1 | ENST00000373271.5 | c.1851G>A | p.Gly617= | synonymous_variant | 17/32 | 1 | A1 | ||
PLCG1 | ENST00000244007.7 | c.1851G>A | p.Gly617= | synonymous_variant | 18/33 | 5 | P3 | ||
PLCG1 | ENST00000465571.2 | n.72G>A | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00807 AC: 1229AN: 152250Hom.: 7 Cov.: 32
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GnomAD3 exomes AF: 0.00824 AC: 2071AN: 251408Hom.: 15 AF XY: 0.00840 AC XY: 1141AN XY: 135880
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GnomAD4 exome AF: 0.0109 AC: 15881AN: 1461776Hom.: 106 Cov.: 34 AF XY: 0.0107 AC XY: 7767AN XY: 727192
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GnomAD4 genome ? AF: 0.00805 AC: 1227AN: 152368Hom.: 7 Cov.: 32 AF XY: 0.00758 AC XY: 565AN XY: 74504
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at