chr1-163203457-G-C

Position:

• chr1-163203457-G-C

Variant summary

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

The NR_110699.1(RGS5-AS1):​n.259-3240G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,210 control chromosomes in the GnomAD database, including 627 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 0.051 (627 hom., cov: 32)
• Consequence: RGS5-AS1 NR_110699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

Genes affected

RGS5-AS1 (HGNC:40504): (RGS5 antisense RNA 1)

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RGS5-AS1	NR_110699.1	n.259-3240G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGS5-AS1	ENST00000415437.1	n.259-3240G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7729 AN: 152094 Hom.: 630 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.00456

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00160

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0509 AC: 7743 AN: 152210 Hom.: 627 Cov.: 32 AF XY: 0.0487 AC XY: 3626 AN XY: 74426

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.00394

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00160

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0376 Hom.: 48

Bravo AF: 0.0572

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2815272; hg19: chr1-163173247;