chr5-64586359-A-G

Variant names:

• chr5-64586359-A-G
• rs10491471
• NM_001029875.3:c.464-8351A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029875.3(RGS7BP):​c.464-8351A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,250 control chromosomes in the GnomAD database, including 138 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 0.036 (138 hom., cov: 32)
• Consequence: RGS7BP NM_001029875.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGS7BP	NM_001029875.3	c.464-8351A>G		intron_variant	Intron 3 of 5	ENST00000334025.3	NP_001025046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGS7BP	ENST00000334025.3	c.464-8351A>G		intron_variant	Intron 3 of 5	1	NM_001029875.3	ENSP00000334851.2
RGS7BP	ENST00000505263.1	n.224-8351A>G		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5437 AN: 152132 Hom.: 138 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0458

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.0413

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

GnomAD4 genome AF: 0.0357 AC: 5437 AN: 152250 Hom.: 138 Cov.: 32 AF XY: 0.0343 AC XY: 2556 AN XY: 74438

African (AFR) AF: 0.0109 AC: 455 AN: 41558

American (AMR) AF: 0.0458 AC: 701 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4822

European-Finnish (FIN) AF: 0.0350 AC: 372 AN: 10616

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0537 AC: 3649 AN: 68008

Other (OTH) AF: 0.0409 AC: 86 AN: 2104

Alfa AF: 0.0503 Hom.: 261

Bravo AF: 0.0356

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		0.40
Mutation Taster		=100/0	polymorphism

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: rs10491471; hg19: chr5-63882186;