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.

Transcripts

RefSeq

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

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs1822285; hg19: chr11-4232627;