rs7531569

Variant names:

• chr1-241305018-C-G
• rs7531569
• NM_001364886.1:c.78+50681G>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS7	NM_001364886.1	MANE Select	c.78+50681G>C		intron	N/A	NP_001351815.1
	RGS7	NM_002924.6		c.78+50681G>C		intron	N/A	NP_002915.3
	RGS7	NM_001282775.2		c.78+50681G>C		intron	N/A	NP_001269704.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS7	ENST00000440928.6	TSL:1 MANE Select	c.78+50681G>C		intron	N/A	ENSP00000404399.2
	RGS7	ENST00000366565.5	TSL:1	c.78+50681G>C		intron	N/A	ENSP00000355523.1
	RGS7	ENST00000366564.5	TSL:1	c.78+50681G>C		intron	N/A	ENSP00000355522.1

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

African (AFR) AF: 0.698 AC: 28935 AN: 41450

American (AMR) AF: 0.432 AC: 6599 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2025 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2512 AN: 5168

South Asian (SAS) AF: 0.544 AC: 2620 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5051 AN: 10546

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35481 AN: 67966

Other (OTH) AF: 0.557 AC: 1173 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.46
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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