11-4211397-C-T

Variant names:

• chr11-4211397-C-T
• rs1822285
• ENST00000528172.1:n.695G>A

Variant summary

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

The ENST00000528172.1(RDXP1):​n.695G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.707 in 749,394 control chromosomes in the GnomAD database, including 191,490 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 0.63 (32605 hom., cov: 32)
  • Exomes 𝑓: 0.73 (158885 hom.)
• Consequence: RDXP1 ENST00000528172.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.94
• Publications: 6 publications found

Genes affected

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

ENSG00000295581 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528172.1. You can select a different transcript below to see updated ACMG assignments.

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
	RDXP1	ENST00000528172.1	TSL:6	n.695G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000295581	ENST00000731035.1		n.1289+3619G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96489 AN: 151966 Hom.: 32600 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.652

GnomAD4 exome AF: 0.726 AC: 433394 AN: 597310 Hom.: 158885 Cov.: 0 AF XY: 0.731 AC XY: 238184 AN XY: 325790

African (AFR) AF: 0.376 AC: 6240 AN: 16580

American (AMR) AF: 0.750 AC: 30087 AN: 40102

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 12890 AN: 19698

East Asian (EAS) AF: 0.747 AC: 26542 AN: 35534

South Asian (SAS) AF: 0.789 AC: 52219 AN: 66194

European-Finnish (FIN) AF: 0.710 AC: 35811 AN: 50404

Middle Eastern (MID) AF: 0.695 AC: 1623 AN: 2336

European-Non Finnish (NFE) AF: 0.733 AC: 246047 AN: 335460

Other (OTH) AF: 0.708 AC: 21935 AN: 31002

GnomAD4 genome AF: 0.635 AC: 96515 AN: 152084 Hom.: 32605 Cov.: 32 AF XY: 0.639 AC XY: 47493 AN XY: 74366

African (AFR) AF: 0.383 AC: 15895 AN: 41452

American (AMR) AF: 0.731 AC: 11175 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3466

East Asian (EAS) AF: 0.716 AC: 3707 AN: 5178

South Asian (SAS) AF: 0.791 AC: 3818 AN: 4826

European-Finnish (FIN) AF: 0.708 AC: 7491 AN: 10578

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50007 AN: 67984

Other (OTH) AF: 0.645 AC: 1362 AN: 2110

Alfa AF: 0.692 Hom.: 74058

Bravo AF: 0.623

Asia WGS AF: 0.690 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		3.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1822285;

hg19: chr11-4232627;