chr14-71925485-A-G

Position:

• chr14-71925485-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024449761.2(RGS6):​c.-21+17051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,186 control chromosomes in the GnomAD database, including 404 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.066 (404 hom., cov: 32)
• Consequence: RGS6 XM_024449761.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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]

ENSG00000266869 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.089 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS6	XM_024449761.2	c.-21+17051A>G		intron_variant			XP_024305529.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266869	ENST00000655301.1	n.842-2798A>G		intron_variant
ENSG00000266869	ENST00000656145.1	n.963-2798A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10017 AN: 152068 Hom.: 404 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.0834

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0658 AC: 10007 AN: 152186 Hom.: 404 Cov.: 32 AF XY: 0.0621 AC XY: 4624 AN XY: 74404

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.0741

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0908

Gnomad4 OTH AF: 0.0830

Alfa AF: 0.0712 Hom.: 57

Bravo AF: 0.0688

Asia WGS AF: 0.0170 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs36339; hg19: chr14-72392202;