rs7531569

Positions:

• chr1-241305018-C-G
• chr1-241305018-C-T

Variant summary

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

The NM_001364886.1(RGS7):​c.78+50681G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,022 control chromosomes in the GnomAD database, including 24,525 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 0.56 (24525 hom., cov: 32)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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]

RGS7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS7	NM_001364886.1	c.78+50681G>C		intron_variant		ENST00000440928.6	NP_001351815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS7	ENST00000440928.6	c.78+50681G>C		intron_variant		1	NM_001364886.1	ENSP00000404399.2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84904 AN: 151904 Hom.: 24498 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.559 AC: 84971 AN: 152022 Hom.: 24525 Cov.: 32 AF XY: 0.553 AC XY: 41074 AN XY: 74316

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.557

Alfa AF: 0.540 Hom.: 2813

Bravo AF: 0.561

Asia WGS AF: 0.546 AC: 1900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.46

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: rs7531569; hg19: chr1-241468318; COSMIC: COSV61906884; COSMIC: COSV61906884;