1-241354678-T-C

Position:

• chr1-241354678-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001350113.2(RGS7):​c.-102A>G variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,096 control chromosomes in the GnomAD database, including 31,469 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 0.63 (31469 hom., cov: 33)
• Consequence: RGS7 NM_001350113.2 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS7	NM_001364886.1	c.78+1021A>G		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+1021A>G		intron_variant		1	NM_001364886.1	ENSP00000404399.2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95475 AN: 151976 Hom.: 31456 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.628 AC: 95513 AN: 152096 Hom.: 31469 Cov.: 33 AF XY: 0.629 AC XY: 46797 AN XY: 74360

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.639

Alfa AF: 0.705 Hom.: 20371

Bravo AF: 0.610

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	17
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341467; hg19: chr1-241517978;