rs12757054

chr1-240776091-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001364886.1(RGS7):c.*129G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 1,150,318 control chromosomes in the GnomAD database, including 3,479 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 0.061 (354 hom., cov: 32)
  • Exomes 𝑓: 0.074 (3125 hom.)
• Consequence: RGS7 NM_001364886.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

RGS7 (HGNC:10003): (regulator of G protein signaling 7) Enables G-protein beta-subunit binding activity and GTPase activator activity. Involved in positive regulation of GTPase activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS7	NM_001364886.1	c.*129G>A		3_prime_UTR_variant	19/19	ENST00000440928.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS7	ENST00000440928.6	c.*129G>A		3_prime_UTR_variant	19/19	1	NM_001364886.1
	ENST00000653456.1	n.956C>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 9276 AN: 152090 Hom.: 353 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0868

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.0602

GnomAD4 exome AF: 0.0742 AC: 74071 AN: 998110 Hom.: 3125 Cov.: 13 AF XY: 0.0754 AC XY: 39049 AN XY: 517592

Gnomad4 AFR exome AF: 0.0371

Gnomad4 AMR exome AF: 0.0389

Gnomad4 ASJ exome AF: 0.0855

Gnomad4 EAS exome AF: 0.0165

Gnomad4 SAS exome AF: 0.0920

Gnomad4 FIN exome AF: 0.0351

Gnomad4 NFE exome AF: 0.0818

Gnomad4 OTH exome AF: 0.0699

GnomAD4 genome AF: 0.0610 AC: 9279 AN: 152208 Hom.: 354 Cov.: 32 AF XY: 0.0596 AC XY: 4435 AN XY: 74440

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0868

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0823

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0778 Hom.: 492

Bravo AF: 0.0599

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	14
Dann	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12757054; hg19: chr1-240939391; COSMIC: COSV58544216; COSMIC: COSV58544216;