rs6667191

Variant names:

• chr1-45517172-A-G
• rs6667191
• NM_181697.3:c.107-1365T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-45517172-A-G
• chr1-45517172-A-T

Variant summary

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

The NM_181697.3(PRDX1):​c.107-1365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,960 control chromosomes in the GnomAD database, including 41,801 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 0.74 (41801 hom., cov: 30)
• Consequence: PRDX1 NM_181697.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 8 publications found

Genes affected

PRDX1 (HGNC:9352): (peroxiredoxin 1) This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein may play an antioxidant protective role in cells, and may contribute to the antiviral activity of CD8(+) T-cells. This protein may have a proliferative effect and play a role in cancer development or progression. Four transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jan 2011]

PRDX1 Gene-Disease associations (from GenCC):

• methylmalonic aciduria and homocystinuria type cblC

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181697.3. 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
	PRDX1	NM_181697.3	MANE Select	c.107-1365T>C		intron	N/A	NP_859048.1	A0A384NPQ2
	PRDX1	NM_001202431.2		c.107-1365T>C		intron	N/A	NP_001189360.1	Q06830
	PRDX1	NM_002574.4		c.107-1365T>C		intron	N/A	NP_002565.1	Q06830

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDX1	ENST00000319248.13	TSL:1 MANE Select	c.107-1365T>C		intron	N/A	ENSP00000361152.5	Q06830
	PRDX1	ENST00000262746.5	TSL:5	c.107-1365T>C		intron	N/A	ENSP00000262746.1	Q06830
	PRDX1	ENST00000424390.2	TSL:2	c.107-1365T>C		intron	N/A	ENSP00000389047.2	Q06830

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112026 AN: 151842 Hom.: 41772 Cov.: 30

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.738 AC: 112107 AN: 151960 Hom.: 41801 Cov.: 30 AF XY: 0.742 AC XY: 55108 AN XY: 74250

African (AFR) AF: 0.818 AC: 33925 AN: 41458

American (AMR) AF: 0.801 AC: 12216 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2549 AN: 3472

East Asian (EAS) AF: 0.942 AC: 4868 AN: 5168

South Asian (SAS) AF: 0.757 AC: 3642 AN: 4814

European-Finnish (FIN) AF: 0.677 AC: 7142 AN: 10546

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45298 AN: 67942

Other (OTH) AF: 0.738 AC: 1550 AN: 2100

Alfa AF: 0.689 Hom.: 6012

Bravo AF: 0.750

Asia WGS AF: 0.857 AC: 2977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.78
PhyloP100		0.099
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: rs6667191; hg19: chr1-45982844;