rs730273

chr20-59678883-A-C

Variant summary

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

The NM_080672.5(PHACTR3):c.119-64224A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,320 control chromosomes in the GnomAD database, including 1,694 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 (1694 hom., cov: 31)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR3	NM_080672.5	c.119-64224A>C		intron_variant		ENST00000371015.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR3	ENST00000371015.6	c.119-64224A>C		intron_variant		1	NM_080672.5	A1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16291 AN: 151202 Hom.: 1682 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0484

Gnomad OTH AF: 0.0944

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

GnomAD4 genome AF: 0.108 AC: 16342 AN: 151320 Hom.: 1694 Cov.: 31 AF XY: 0.103 AC XY: 7649 AN XY: 73926

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0484

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.0866 Hom.: 136

Bravo AF: 0.119

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.044
Dann	Benign	0.45

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: rs730273; hg19: chr20-58253938;