rs9636470

Variant names:

• chr2-87866942-T-C
• rs9636470
• XM_017004845.2:c.307-48319A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-87866942-T-C
• chr2-87866942-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XM_017004845.2(RGPD2):​c.307-48319A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 100,014 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.13 (0 hom., cov: 30)
• Consequence: RGPD2 XM_017004845.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 5 publications found

Genes affected

RGPD2 (HGNC:32415): (RANBP2 like and GRIP domain containing 2) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Variant has high frequency in the EAS (0.202) population. However there is too low homozygotes in high coverage region: (expected more than 454, got 0).
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.135 AC: 13477 AN: 99894 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0380

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.135 AC: 13484 AN: 100014 Hom.: 0 Cov.: 30 AF XY: 0.0710 AC XY: 3440 AN XY: 48436

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0380 AC: 1254 AN: 33010

American (AMR) AF: 0.155 AC: 1437 AN: 9296

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 457 AN: 2012

East Asian (EAS) AF: 0.216 AC: 631 AN: 2918

South Asian (SAS) AF: 0.136 AC: 402 AN: 2962

European-Finnish (FIN) AF: 0.108 AC: 703 AN: 6492

Middle Eastern (MID) AF: 0.0990 AC: 20 AN: 202

European-Non Finnish (NFE) AF: 0.202 AC: 8318 AN: 41206

Other (OTH) AF: 0.144 AC: 195 AN: 1350

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0779 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9636470; hg19: chr2-88166461;