NM_001005339.2:c.50-83C>T

Variant names:

• chr10-119527507-G-A
• rs3009921
• NM_001005339.2:c.50-83C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001005339.2(RGS10):​c.50-83C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.998 in 1,000,102 control chromosomes in the GnomAD database, including 498,223 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.99 (75054 hom., cov: 33)
  • Exomes 𝑓: 1.0 (423169 hom.)
• Consequence: RGS10 NM_001005339.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0530
• Publications: 3 publications found

Genes affected

RGS10 (HGNC:9992): (regulator of G protein signaling 10) Regulator of G protein signaling (RGS) family members are regulatory molecules that act as GTPase activating proteins (GAPs) for G alpha subunits of heterotrimeric G proteins. RGS proteins are able to deactivate G protein subunits of the Gi alpha, Go alpha and Gq alpha subtypes. They drive G proteins into their inactive GDP-bound forms. Regulator of G protein signaling 10 belongs to this family. All RGS proteins share a conserved 120-amino acid sequence termed the RGS domain. This protein associates specifically with the activated forms of the two related G-protein subunits, G-alphai3 and G-alphaz but fails to interact with the structurally and functionally distinct G-alpha subunits. Regulator of G protein signaling 10 protein is localized in the nucleus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-119527507-G-A is Benign according to our data. Variant chr10-119527507-G-A is described in ClinVar as Benign. ClinVar VariationId is 2688104.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005339.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS10	NM_001005339.2	MANE Select	c.50-83C>T		intron	N/A	NP_001005339.1	O43665-3
	RGS10	NM_002925.4		c.8-83C>T		intron	N/A	NP_002916.1	O43665-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGS10	ENST00000369103.3	TSL:1 MANE Select	c.50-83C>T		intron	N/A	ENSP00000358099.2	O43665-3
	RGS10	ENST00000392865.5	TSL:1	c.8-83C>T		intron	N/A	ENSP00000376605.1	O43665-2
	RGS10	ENST00000949340.1		c.50-83C>T		intron	N/A	ENSP00000619399.1

Frequencies

GnomAD3 genomes AF: 0.993 AC: 151099 AN: 152226 Hom.: 74997 Cov.: 33

Gnomad AFR AF: 0.974

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.998

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.998

GnomAD4 exome AF: 0.999 AC: 847039 AN: 847758 Hom.: 423169 Cov.: 11 AF XY: 0.999 AC XY: 442569 AN XY: 442878

African (AFR) AF: 0.974 AC: 21343 AN: 21920

American (AMR) AF: 0.999 AC: 43149 AN: 43200

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 21224 AN: 21224

East Asian (EAS) AF: 1.00 AC: 36746 AN: 36746

South Asian (SAS) AF: 1.00 AC: 71653 AN: 71656

European-Finnish (FIN) AF: 1.00 AC: 46633 AN: 46634

Middle Eastern (MID) AF: 0.999 AC: 4330 AN: 4334

European-Non Finnish (NFE) AF: 1.00 AC: 561683 AN: 561696

Other (OTH) AF: 0.998 AC: 40278 AN: 40348

GnomAD4 genome AF: 0.993 AC: 151215 AN: 152344 Hom.: 75054 Cov.: 33 AF XY: 0.993 AC XY: 73949 AN XY: 74490

African (AFR) AF: 0.974 AC: 40488 AN: 41572

American (AMR) AF: 0.998 AC: 15276 AN: 15310

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 1.00 AC: 4826 AN: 4826

European-Finnish (FIN) AF: 1.00 AC: 10628 AN: 10628

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68038 AN: 68044

Other (OTH) AF: 0.998 AC: 2105 AN: 2110

Alfa AF: 0.992 Hom.: 10460

Bravo AF: 0.991

Asia WGS AF: 0.999 AC: 3476 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.053
PromoterAI		-0.045	Neutral
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: rs3009921; hg19: chr10-121287019;