1-240891165-A-G

Position:

• chr1-240891165-A-G

Variant summary

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

The NM_001364886.1(RGS7):​c.386-21046T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,956 control chromosomes in the GnomAD database, including 25,311 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 0.57 (25311 hom., cov: 31)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS7	NM_001364886.1	c.386-21046T>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.386-21046T>C		intron_variant		1	NM_001364886.1	ENSP00000404399.2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86654 AN: 151838 Hom.: 25278 Cov.: 31

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.571 AC: 86739 AN: 151956 Hom.: 25311 Cov.: 31 AF XY: 0.568 AC XY: 42204 AN XY: 74278

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.527

Alfa AF: 0.442 Hom.: 1311

Bravo AF: 0.577

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
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: rs261809; hg19: chr1-241054465;