Genetic Variant RDXP1:n.695G>C (chr11-4211397-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000528172.1(RDXP1):n.695G>C variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RDXP1
ENST00000528172.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.94

Publications

6 publications found

Variant links:

Genes affected

RDXP1 (HGNC:9945): (RDX pseudogene 1)

RDXP1 links:

ENSG00000295581 (HGNC:):

ENSG00000295581 links:

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ACMG classification

Classification was made for transcript

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

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RDXP1		n.4211397C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RDXP1	ENST00000528172.1 link	n.695G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000295581	ENST00000731035.1 link	n.1289+3619G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

597872

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

326098

African (AFR)

AF:

0.00

AC:

AN:

16602

American (AMR)

AF:

0.00

AC:

AN:

40176

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19722

East Asian (EAS)

AF:

0.00

AC:

AN:

35574

South Asian (SAS)

AF:

0.00

AC:

AN:

66254

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50438

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2336

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

335738

Other (OTH)

AF:

0.00

AC:

AN:

31032

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

5.6

(source)

DANN

Benign

0.80

PhyloP100

3.9

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over