rs10495476

Variant names:

• chr1-240843653-C-A
• rs10495476
• NM_001364886.1:c.610-16481G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-240843653-C-A
• chr1-240843653-C-G
• chr1-240843653-C-T

Variant summary

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

The NM_001364886.1(RGS7):​c.610-16481G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,006 control chromosomes in the GnomAD database, including 35,083 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 0.68 (35083 hom., cov: 32)
• Consequence: RGS7 NM_001364886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS7	NM_001364886.1	c.610-16481G>T		intron_variant	Intron 9 of 18	ENST00000440928.6	NP_001351815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS7	ENST00000440928.6	c.610-16481G>T		intron_variant	Intron 9 of 18	1	NM_001364886.1	ENSP00000404399.2

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102585 AN: 151888 Hom.: 35069 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.675 AC: 102631 AN: 152006 Hom.: 35083 Cov.: 32 AF XY: 0.668 AC XY: 49634 AN XY: 74290

African (AFR) AF: 0.583 AC: 24142 AN: 41426

American (AMR) AF: 0.685 AC: 10469 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3248 AN: 5174

South Asian (SAS) AF: 0.630 AC: 3038 AN: 4820

European-Finnish (FIN) AF: 0.644 AC: 6787 AN: 10546

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50324 AN: 67974

Other (OTH) AF: 0.679 AC: 1431 AN: 2108

Alfa AF: 0.721 Hom.: 128803

Bravo AF: 0.676

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.53
PhyloP100		0.071
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: rs10495476; hg19: chr1-241006953;