20-58269248-A-C

Variant names:

• chr20-58269248-A-C
• rs6128297
• ENST00000244070.9:n.464+2115T>G

Variant summary

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

The ENST00000244070.9(ENSG00000291067):​n.464+2115T>G variant causes a intron 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: ENSG00000291067 ENST00000244070.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 1 publications found

Genes affected

ENSG00000291067 (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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000244070.9. 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
	PPP4R1L	NR_003505.3		n.306+3521T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291067	ENST00000244070.9	TSL:1	n.464+2115T>G		intron	N/A
	ENSG00000291067	ENST00000495058.7	TSL:1	n.471+2115T>G		intron	N/A
	PPP4R1L	ENST00000334187.12	TSL:6	n.336+2115T>G		intron	N/A

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

African (AFR) AF: 0.989 AC: 41103 AN: 41554

American (AMR) AF: 0.958 AC: 14661 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3328 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5174 AN: 5176

South Asian (SAS) AF: 0.967 AC: 4663 AN: 4820

European-Finnish (FIN) AF: 0.960 AC: 10191 AN: 10612

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64218 AN: 68026

Other (OTH) AF: 0.956 AC: 2020 AN: 2114

Alfa AF: 0.950 Hom.: 99531

Bravo AF: 0.963

Asia WGS AF: 0.981 AC: 3411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.23
PhyloP100		-2.5
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: rs6128297; hg19: chr20-56844304;