chr19-3157796-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002068.4(GNA15):c.813C>T(p.Ser271=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000815 in 1,613,010 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0043 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00046 ( 5 hom. )
Consequence
GNA15
NM_002068.4 synonymous
NM_002068.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.16
Genes affected
GNA15 (HGNC:4383): (G protein subunit alpha 15) Enables G protein-coupled receptor binding activity. Involved in positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway. Predicted to be located in plasma membrane. Predicted to be part of heterotrimeric G-protein complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.79).
BP6
?
Variant 19-3157796-C-T is Benign according to our data. Variant chr19-3157796-C-T is described in ClinVar as [Benign]. Clinvar id is 788012.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.16 with no splicing effect.
BS2
?
High AC in GnomAd at 645 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNA15 | NM_002068.4 | c.813C>T | p.Ser271= | synonymous_variant | 6/7 | ENST00000262958.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNA15 | ENST00000262958.4 | c.813C>T | p.Ser271= | synonymous_variant | 6/7 | 1 | NM_002068.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00424 AC: 645AN: 152176Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00123 AC: 310AN: 251494Hom.: 6 AF XY: 0.000809 AC XY: 110AN XY: 135922
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GnomAD4 exome AF: 0.000457 AC: 667AN: 1460716Hom.: 5 Cov.: 30 AF XY: 0.000365 AC XY: 265AN XY: 726738
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GnomAD4 genome ? AF: 0.00425 AC: 648AN: 152294Hom.: 3 Cov.: 32 AF XY: 0.00412 AC XY: 307AN XY: 74474
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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 | Dec 04, 2018 | - - |
Computational scores
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Name
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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