NM_001364886.1:c.78+64492A>G

Variant names:

• chr1-241291207-T-C
• rs6697953
• NM_001364886.1:c.78+64492A>G

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+64492A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,090 control chromosomes in the GnomAD database, including 36,689 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 0.69 (36689 hom., cov: 32)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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+64492A>G		intron	N/A	NP_001351815.1
	RGS7	NM_002924.6		c.78+64492A>G		intron	N/A	NP_002915.3
	RGS7	NM_001282775.2		c.78+64492A>G		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+64492A>G		intron	N/A	ENSP00000404399.2
	RGS7	ENST00000366565.5	TSL:1	c.78+64492A>G		intron	N/A	ENSP00000355523.1
	RGS7	ENST00000366564.5	TSL:1	c.78+64492A>G		intron	N/A	ENSP00000355522.1

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104667 AN: 151972 Hom.: 36661 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.689 AC: 104738 AN: 152090 Hom.: 36689 Cov.: 32 AF XY: 0.699 AC XY: 51960 AN XY: 74372

African (AFR) AF: 0.559 AC: 23151 AN: 41436

American (AMR) AF: 0.727 AC: 11111 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2123 AN: 3470

East Asian (EAS) AF: 0.852 AC: 4405 AN: 5168

South Asian (SAS) AF: 0.806 AC: 3890 AN: 4826

European-Finnish (FIN) AF: 0.860 AC: 9114 AN: 10598

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48530 AN: 67982

Other (OTH) AF: 0.680 AC: 1437 AN: 2112

Alfa AF: 0.661 Hom.: 5697

Bravo AF: 0.672

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.76
PhyloP100		-0.48
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: rs6697953; hg19: chr1-241454507;