rs272629

chr5-64511251-G-A

Variant summary

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

The NM_001029875.3(RGS7BP):c.332+3374G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,082 control chromosomes in the GnomAD database, including 13,273 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 0.41 (13273 hom., cov: 33)
• Consequence: RGS7BP NM_001029875.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

RGS7BP (HGNC:23271): (regulator of G protein signaling 7 binding protein) This gene encodes a protein that binds to all members of the R7 subfamily of regulators of G protein signaling and regulates their translocation between the nucleus and the plasma membrane. The encoded protein could be regulated by reversible palmitoylation, which anchors it to the plasma membrane. Depalmitoylation localizes the protein to the nucleus. Polymorphisms in this gene may be associated with risk of aspirin-exacerbated respiratory disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RGS7BP	NM_001029875.3	c.332+3374G>A		intron_variant		ENST00000334025.3
RGS7BP	XM_005248502.5	c.332+3374G>A		intron_variant
RGS7BP	XR_948251.4	n.942+3374G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGS7BP	ENST00000334025.3	c.332+3374G>A		intron_variant		1	NM_001029875.3	P1
RGS7BP	ENST00000508162.1	n.533+4462G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62415 AN: 151964 Hom.: 13247 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.411 AC: 62485 AN: 152082 Hom.: 13273 Cov.: 33 AF XY: 0.414 AC XY: 30796 AN XY: 74346

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.386

Alfa AF: 0.425 Hom.: 14076

Bravo AF: 0.410

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs272629; hg19: chr5-63807078;