rs10494390

Variant names:

• chr1-163251007-T-A
• NM_001414472.1:c.-4-2409A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-163251007-T-A
• chr1-163251007-T-C
• chr1-163251007-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001414472.1(RGS5):​c.-4-2409A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RGS5 NM_001414472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

Genes affected

RGS5 (HGNC:10001): (regulator of G protein signaling 5) This locus represents naturally occurring readthrough transcription between the neighboring LOC127814295 (uncharacterized LOC127814295) and RGS5 (regulator of G-protein signaling 5) genes on chromosome 1. Some variants of the readthrough transcript encode novel proteins with unique N-termini. [provided by RefSeq, Nov 2022]

ENSG00000232995 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS5	NM_001414472.1	c.-4-2409A>T		intron_variant	Intron 2 of 6		NP_001401401.1
RGS5	NM_001414473.1	c.-4-2409A>T		intron_variant	Intron 4 of 8		NP_001401402.1
RGS5	NM_001414474.1	c.-4-2409A>T		intron_variant	Intron 3 of 7		NP_001401403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS5	ENST00000618415.4	c.-281+55226A>T		intron_variant	Intron 2 of 5	4		ENSP00000480891.1
ENSG00000232995	ENST00000427213.5	n.229-2301A>T		intron_variant	Intron 2 of 2	3
RGS5	ENST00000428971.2	n.446+55226A>T		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-163220797;