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rs9636470

chr2-87866942-T-Cchr2-87866942-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
RGPD2XM_017004845.2 linkuse as main transcriptc.307-48319A>G intron_variant
RGPD2XM_047445734.1 linkuse as main transcriptc.232-48319A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.135
AC:
13477
AN:
99894
Hom.:
0
Cov.:
30
show subpopulations
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.135
AC:
13484
AN:
100014
Hom.:
0
Cov.:
30
AF XY:
0.0710
AC XY:
3440
AN XY:
48436
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9636470; hg19: chr2-88166461; API