1-173479356-A-G

Variant names:

• chr1-173479356-A-G
• rs9425723
• NM_004905.3:c.95+1864A>G

Variant summary

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

The NM_004905.3(PRDX6):​c.95+1864A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,746 control chromosomes in the GnomAD database, including 14,597 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 0.38 (14597 hom., cov: 32)
• Consequence: PRDX6 NM_004905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 3 publications found

Genes affected

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]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3	c.95+1864A>G		intron_variant	Intron 1 of 4	ENST00000340385.6	NP_004896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6	c.95+1864A>G		intron_variant	Intron 1 of 4	1	NM_004905.3	ENSP00000342026.5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57980 AN: 151628 Hom.: 14547 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.383 AC: 58099 AN: 151746 Hom.: 14597 Cov.: 32 AF XY: 0.378 AC XY: 28049 AN XY: 74172

African (AFR) AF: 0.710 AC: 29300 AN: 41260

American (AMR) AF: 0.266 AC: 4066 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.591 AC: 3032 AN: 5126

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2056 AN: 10534

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16340 AN: 67946

Other (OTH) AF: 0.337 AC: 711 AN: 2108

Alfa AF: 0.324 Hom.: 1313

Bravo AF: 0.406

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		-0.054
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9425723; hg19: chr1-173448495;