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

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

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGPD2	XM_017004845.2	c.307-48319A>G		intron_variant	Intron 4 of 25		XP_016860334.2
RGPD2	XM_047445734.1	c.232-48319A>G		intron_variant	Intron 3 of 24		XP_047301690.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0380

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0779 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9636470; hg19: chr2-88166461;