rs10131300
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001204424.2(RGS6):c.537-85C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 979,808 control chromosomes in the GnomAD database, including 246,975 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.71 ( 38324 hom., cov: 32)
Exomes 𝑓: 0.71 ( 208651 hom. )
Consequence
RGS6
NM_001204424.2 intron
NM_001204424.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.144
Genes affected
RGS6 (HGNC:10002): (regulator of G protein signaling 6) This gene encodes a member of the RGS (regulator of G protein signaling) family of proteins, which are defined by the presence of a RGS domain that confers the GTPase-activating activity of these proteins toward certain G alpha subunits. This protein also belongs to a subfamily of RGS proteins characterized by the presence of DEP and GGL domains, the latter a G beta 5-interacting domain. The RGS proteins negatively regulate G protein signaling, and may modulate neuronal, cardiovascular, lymphocytic activities, and cancer risk. Many alternatively spliced transcript variants encoding different isoforms with long or short N-terminal domains, complete or incomplete GGL domains, and distinct C-terminal domains, have been described for this gene, however, the full-length nature of some of these variants is not known.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 14-72472787-C-A is Benign according to our data. Variant chr14-72472787-C-A is described in ClinVar as [Benign]. Clinvar id is 1243968.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS6 | NM_001204424.2 | c.537-85C>A | intron_variant | ENST00000553525.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS6 | ENST00000553525.6 | c.537-85C>A | intron_variant | 2 | NM_001204424.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.707 AC: 107417AN: 151968Hom.: 38295 Cov.: 32
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GnomAD4 exome AF: 0.706 AC: 584278AN: 827722Hom.: 208651 AF XY: 0.707 AC XY: 305872AN XY: 432922
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GnomAD4 genome ? AF: 0.707 AC: 107495AN: 152086Hom.: 38324 Cov.: 32 AF XY: 0.713 AC XY: 53009AN XY: 74346
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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 | GeneDx | Jul 21, 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