20-59824364-G-T

Variant summary

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

The NM_080672.5(PHACTR3):c.1329-12141G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,274 control chromosomes in the GnomAD database, including 423 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 0.051 (423 hom., cov: 32)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

PHACTR3 (HGNC:15833): (phosphatase and actin regulator 3) This gene encodes a member of the phosphatase and actin regulator protein family. The encoded protein is associated with the nuclear scaffold in proliferating cells, and binds to actin and the catalytic subunit of protein phosphatase-1, suggesting that it functions as a regulatory subunit of protein phosphatase-1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR3	NM_080672.5	c.1329-12141G>T		intron_variant		ENST00000371015.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR3	ENST00000371015.6	c.1329-12141G>T		intron_variant		1	NM_080672.5	A1

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7730 AN: 152156 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0393

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0508 AC: 7736 AN: 152274 Hom.: 423 Cov.: 32 AF XY: 0.0558 AC XY: 4153 AN XY: 74448

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0393

Gnomad4 OTH AF: 0.0515

Alfa AF: 0.0435 Hom.: 276

Bravo AF: 0.0553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs746219; hg19: chr20-58399419;