chr1-241020312-A-G

Position:

• chr1-241020312-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.176-37183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,042 control chromosomes in the GnomAD database, including 15,602 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 0.39 (15602 hom., cov: 32)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS7	NM_001364886.1	c.176-37183T>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.176-37183T>C		intron_variant		1	NM_001364886.1	ENSP00000404399.2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58902 AN: 151924 Hom.: 15554 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.388 AC: 59009 AN: 152042 Hom.: 15602 Cov.: 32 AF XY: 0.385 AC XY: 28628 AN XY: 74338

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.367

Alfa AF: 0.265 Hom.: 8129

Bravo AF: 0.416

Asia WGS AF: 0.342 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.76

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: rs601675; hg19: chr1-241183612;