1-163210798-T-C

Position:

• chr1-163210798-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001414472.1(RGS5):​c.65+37732A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,142 control chromosomes in the GnomAD database, including 41,575 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 0.73 (41575 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: RGS5 NM_001414472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86

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]

RGS5-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS5	NM_001414472.1	c.65+37732A>G		intron_variant			NP_001401401.1
RGS5	NM_001414473.1	c.65+37732A>G		intron_variant			NP_001401402.1
RGS5	NM_001414474.1	c.65+37732A>G		intron_variant			NP_001401403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS5	ENST00000367903.7	c.69+6728A>G		intron_variant		3		ENSP00000356879.3
RGS5	ENST00000618415.4	c.-280-42430A>G		intron_variant		4		ENSP00000480891.1
RGS5-AS1	ENST00000415437.1	n.408T>C		non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111094 AN: 152022 Hom.: 41527 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.718

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.731 AC: 111193 AN: 152142 Hom.: 41575 Cov.: 32 AF XY: 0.721 AC XY: 53622 AN XY: 74368

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.717

Alfa AF: 0.729 Hom.: 8780

Bravo AF: 0.733

Asia WGS AF: 0.586 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2940677; hg19: chr1-163180588;