rs7544372

Variant names:

• chr1-240824454-C-T
• rs7544372
• NM_001364886.1:c.684+2644G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364886.1(RGS7):​c.684+2644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,196 control chromosomes in the GnomAD database, including 47,712 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 0.78 (47712 hom., cov: 33)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 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

LOC124904602 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.875 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.684+2644G>A		intron	N/A	NP_001351815.1
	RGS7	NM_002924.6		c.684+2644G>A		intron	N/A	NP_002915.3
	RGS7	NM_001282775.2		c.684+2644G>A		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.684+2644G>A		intron	N/A	ENSP00000404399.2
	RGS7	ENST00000366565.5	TSL:1	c.684+2644G>A		intron	N/A	ENSP00000355523.1
	RGS7	ENST00000366564.5	TSL:1	c.684+2644G>A		intron	N/A	ENSP00000355522.1

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119185 AN: 152078 Hom.: 47704 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.783 AC: 119217 AN: 152196 Hom.: 47712 Cov.: 33 AF XY: 0.781 AC XY: 58124 AN XY: 74406

African (AFR) AF: 0.614 AC: 25456 AN: 41488

American (AMR) AF: 0.796 AC: 12183 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2858 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3401 AN: 5168

South Asian (SAS) AF: 0.749 AC: 3619 AN: 4832

European-Finnish (FIN) AF: 0.854 AC: 9051 AN: 10604

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.881 AC: 59915 AN: 68018

Other (OTH) AF: 0.793 AC: 1676 AN: 2114

Alfa AF: 0.836 Hom.: 98707

Bravo AF: 0.770

Asia WGS AF: 0.673 AC: 2341 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	0.98
DANN	Benign	0.71
PhyloP100		-1.0
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: rs7544372; hg19: chr1-240987754;