rs6128297

chr20-58269248-A-Cchr20-58269248-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003505.3(PPP4R1L):n.306+3521T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,274 control chromosomes in the GnomAD database, including 70,558 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 0.96 (70558 hom., cov: 31)
• Consequence: PPP4R1L NR_003505.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

(HGNC:):

PPP4R1L (HGNC:15755): (protein phosphatase 4 regulatory subunit 1 like (pseudogene)) Predicted to enable protein phosphatase regulator activity. Predicted to be involved in protein dephosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP4R1L	NR_003505.3	n.306+3521T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP4R1L	ENST00000334187.12	n.336+2115T>G		intron_variant, non_coding_transcript_variant
	ENST00000650934.1	n.461+2115T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146416 AN: 152156 Hom.: 70500 Cov.: 31

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.962 AC: 146533 AN: 152274 Hom.: 70558 Cov.: 31 AF XY: 0.963 AC XY: 71710 AN XY: 74458

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.958

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.956

Alfa AF: 0.947 Hom.: 66944

Bravo AF: 0.963

Asia WGS AF: 0.981 AC: 3411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6128297; hg19: chr20-56844304;