11-4211397-C-T

Position:

• chr11-4211397-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RDXP1	ENST00000528172.1	n.695G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.376

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.654

Gnomad4 EAS exome AF: 0.747

Gnomad4 SAS exome AF: 0.789

Gnomad4 FIN exome AF: 0.710

Gnomad4 NFE exome AF: 0.733

Gnomad4 OTH exome AF: 0.708

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.645

Alfa AF: 0.714 Hom.: 46713

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822285; hg19: chr11-4232627;