rs1047635

Variant names:

• chr1-52608860-C-A
• rs1047635
• NM_015696.5:c.*435C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-52608860-C-A
• chr1-52608860-C-G
• chr1-52608860-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_015696.5(GPX7):​c.*435C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,804 control chromosomes in the GnomAD database, including 20,858 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 0.51 (20744 hom., cov: 33)
  • Exomes 𝑓: 0.54 (114 hom.)
• Consequence: GPX7 NM_015696.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 26 publications found

Genes affected

GPX7 (HGNC:4559): (glutathione peroxidase 7) Enables catalase activity. Predicted to be involved in cellular response to oxidative stress. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPX7	NM_015696.5	c.*435C>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000361314.5	NP_056511.2
GPX7	XM_047418560.1	c.*435C>A		3_prime_UTR_variant	Exon 3 of 3		XP_047274516.1
GPX7	XM_047418564.1	c.*435C>A		3_prime_UTR_variant	Exon 3 of 3		XP_047274520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPX7	ENST00000361314.5	c.*435C>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_015696.5	ENSP00000354677.4

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77903 AN: 151894 Hom.: 20736 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.550

GnomAD4 exome AF: 0.539 AC: 427 AN: 792 Hom.: 114 Cov.: 0 AF XY: 0.510 AC XY: 211 AN XY: 414

African (AFR) AF: 0.375 AC: 6 AN: 16

American (AMR) AF: 0.667 AC: 8 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 9 AN: 14

East Asian (EAS) AF: 0.500 AC: 2 AN: 4

South Asian (SAS) AF: 0.700 AC: 7 AN: 10

European-Finnish (FIN) AF: 0.562 AC: 246 AN: 438

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.518 AC: 142 AN: 274

Other (OTH) AF: 0.292 AC: 7 AN: 24

GnomAD4 genome AF: 0.513 AC: 77928 AN: 152012 Hom.: 20744 Cov.: 33 AF XY: 0.519 AC XY: 38586 AN XY: 74320

African (AFR) AF: 0.355 AC: 14721 AN: 41452

American (AMR) AF: 0.623 AC: 9526 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2069 AN: 3466

East Asian (EAS) AF: 0.764 AC: 3949 AN: 5170

South Asian (SAS) AF: 0.640 AC: 3085 AN: 4820

European-Finnish (FIN) AF: 0.572 AC: 6036 AN: 10556

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36799 AN: 67944

Other (OTH) AF: 0.552 AC: 1163 AN: 2108

Alfa AF: 0.534 Hom.: 83346

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		0.044
Mutation Taster		=99/1	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: rs1047635; hg19: chr1-53074532;