rs1182532

chr20-59818490-C-A

Variant summary

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

The NM_080672.5(PHACTR3):c.1328+12296C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,240 control chromosomes in the GnomAD database, including 1,207 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 (1207 hom., cov: 33)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR3	NM_080672.5	c.1328+12296C>A		intron_variant		ENST00000371015.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR3	ENST00000371015.6	c.1328+12296C>A		intron_variant		1	NM_080672.5	A1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16799 AN: 152122 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.110 AC: 16795 AN: 152240 Hom.: 1207 Cov.: 33 AF XY: 0.109 AC XY: 8122 AN XY: 74420

Gnomad4 AFR AF: 0.0266

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0643

Gnomad4 SAS AF: 0.0575

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.131

Alfa AF: 0.134 Hom.: 380

Bravo AF: 0.106

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.66

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: rs1182532; hg19: chr20-58393545;