rs716743

chr1-240849479-T-A

Variant summary

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

The NM_001364886.1(RGS7):c.609+19108A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,192 control chromosomes in the GnomAD database, including 49,638 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 0.80 (49638 hom., cov: 32)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS7	NM_001364886.1	c.609+19108A>T		intron_variant		ENST00000440928.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS7	ENST00000440928.6	c.609+19108A>T		intron_variant		1	NM_001364886.1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122283 AN: 152072 Hom.: 49598 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.804 AC: 122376 AN: 152192 Hom.: 49638 Cov.: 32 AF XY: 0.798 AC XY: 59327 AN XY: 74386

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.776

Alfa AF: 0.804 Hom.: 6161

Bravo AF: 0.811

Asia WGS AF: 0.650 AC: 2267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.8
Dann	Benign	0.80

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: rs716743; hg19: chr1-241012779;