rs8735

Variant names:

• chr10-80432957-T-A
• rs8735
• NM_032333.5:c.*858T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-80432957-T-A
• chr10-80432957-T-C
• chr10-80432957-T-G

Variant summary

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

The NM_032333.5(PRXL2A):​c.*858T>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 0.349 in 152,058 control chromosomes in the GnomAD database, including 10,991 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 0.35 (10991 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PRXL2A NM_032333.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 13 publications found

Genes affected

PRXL2A (HGNC:28651): (peroxiredoxin like 2A) Enables antioxidant activity. Involved in regulation of osteoclast differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032333.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRXL2A	NM_032333.5	MANE Select	c.*858T>A		3_prime_UTR	Exon 6 of 6	NP_115709.3
	PRXL2A	NM_001243778.2		c.*858T>A		3_prime_UTR	Exon 6 of 6	NP_001230707.1
	PRXL2A	NM_001243779.2		c.*858T>A		3_prime_UTR	Exon 6 of 6	NP_001230708.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRXL2A	ENST00000606162.6	TSL:1 MANE Select	c.*858T>A		3_prime_UTR	Exon 6 of 6	ENSP00000482445.1
	PRXL2A	ENST00000372187.9	TSL:1	c.*858T>A		3_prime_UTR	Exon 6 of 6	ENSP00000361261.5
	PRXL2A	ENST00000372181.1	TSL:2	c.*858T>A		3_prime_UTR	Exon 5 of 5	ENSP00000361254.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53044 AN: 151940 Hom.: 10988 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.386

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.349 AC: 53049 AN: 152058 Hom.: 10991 Cov.: 32 AF XY: 0.355 AC XY: 26388 AN XY: 74352

African (AFR) AF: 0.143 AC: 5923 AN: 41510

American (AMR) AF: 0.406 AC: 6197 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4277 AN: 5168

South Asian (SAS) AF: 0.339 AC: 1635 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4780 AN: 10534

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27710 AN: 67968

Other (OTH) AF: 0.385 AC: 810 AN: 2104

Alfa AF: 0.226 Hom.: 585

Bravo AF: 0.342

Asia WGS AF: 0.497 AC: 1724 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.6
DANN	Benign	0.80
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs8735; hg19: chr10-82192713;