1-173489187-C-T

Variant names:

• chr1-173489187-C-T
• rs33951697
• XR_007066738.1:n.3620G>A

Variant summary

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

The XR_007066738.1(LOC124904456):​n.3620G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,138 control chromosomes in the GnomAD database, including 2,009 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 0.15 (2009 hom., cov: 32)
• Consequence: LOC124904456 XR_007066738.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 4 publications found

Genes affected

LOC124904456 (HGNC:):

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

PRDX6 (HGNC:16753): (peroxiredoxin 6) The protein encoded by this gene is a member of the thiol-specific antioxidant protein family. This protein is a bifunctional enzyme with two distinct active sites. It is involved in redox regulation of the cell; it can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. It may play a role in the regulation of phospholipid turnover as well as in protection against oxidative injury. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669220.1. 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
	PRDX6-AS1	ENST00000669220.1		n.117+104G>A		intron	N/A
	PRDX6-AS1	ENST00000778745.1		n.112+104G>A		intron	N/A
	PRDX6-AS1	ENST00000778747.1		n.114+104G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22548 AN: 152020 Hom.: 2008 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.156

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.148 AC: 22561 AN: 152138 Hom.: 2009 Cov.: 32 AF XY: 0.148 AC XY: 10982 AN XY: 74360

African (AFR) AF: 0.0537 AC: 2230 AN: 41536

American (AMR) AF: 0.162 AC: 2469 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3462

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5164

South Asian (SAS) AF: 0.120 AC: 579 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10566

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12658 AN: 67986

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.170 Hom.: 465

Bravo AF: 0.148

Asia WGS AF: 0.189 AC: 655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.51
DANN	Benign	0.48
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs33951697; hg19: chr1-173458326; COSMIC: COSV107424399;