rs325349

Variant names:

• chr5-27410683-A-G
• rs325349
• ENST00000510512.3:n.508+1923T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-27410683-A-G
• chr5-27410683-A-T

Variant summary

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

The ENST00000510512.3(ENSG00000248490):​n.508+1923T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,078 control chromosomes in the GnomAD database, including 3,259 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 0.11 (3259 hom., cov: 32)
• Consequence: ENSG00000248490 ENST00000510512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 1 publications found

Genes affected

ENSG00000248490 (HGNC:):

PURPL (HGNC:48995): (p53 upregulated regulator of p53 levels)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374695	XR_925873.2	n.505+1923T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248490	ENST00000510512.3	n.508+1923T>C		intron_variant	Intron 4 of 4	3
PURPL	ENST00000650981.1	n.490+3565A>G		intron_variant	Intron 3 of 9
PURPL	ENST00000651409.1	n.775+3565A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17333 AN: 151960 Hom.: 3238 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00122

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.114 AC: 17399 AN: 152078 Hom.: 3259 Cov.: 32 AF XY: 0.111 AC XY: 8268 AN XY: 74378

African (AFR) AF: 0.398 AC: 16459 AN: 41404

American (AMR) AF: 0.0425 AC: 649 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.000289 AC: 1 AN: 3466

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5156

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00122 AC: 83 AN: 68014

Other (OTH) AF: 0.0856 AC: 180 AN: 2102

Alfa AF: 0.157 Hom.: 1609

Bravo AF: 0.130

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	12
DANN	Benign	0.57
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs325349; hg19: chr5-27410790;