rs912767

Variant names:

• chr1-173487306-A-G
• rs912767
• NM_004905.3:c.547-429A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-173487306-A-G
• chr1-173487306-A-T

Variant summary

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

The NM_004905.3(PRDX6):​c.547-429A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,152 control chromosomes in the GnomAD database, including 3,577 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 0.21 (3577 hom., cov: 32)
• Consequence: PRDX6 NM_004905.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX6	NM_004905.3	c.547-429A>G		intron_variant	Intron 4 of 4	ENST00000340385.6	NP_004896.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX6	ENST00000340385.6	c.547-429A>G		intron_variant	Intron 4 of 4	1	NM_004905.3	ENSP00000342026.5

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31978 AN: 152032 Hom.: 3567 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.211 AC: 32036 AN: 152152 Hom.: 3577 Cov.: 32 AF XY: 0.208 AC XY: 15488 AN XY: 74392

African (AFR) AF: 0.266 AC: 11054 AN: 41486

American (AMR) AF: 0.188 AC: 2879 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1619 AN: 5176

South Asian (SAS) AF: 0.117 AC: 566 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10588

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12713 AN: 67988

Other (OTH) AF: 0.208 AC: 440 AN: 2116

Alfa AF: 0.202 Hom.: 522

Bravo AF: 0.220

Asia WGS AF: 0.210 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.78
PhyloP100		-0.72
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: rs912767; hg19: chr1-173456445;