rs1182531

Positions:

• chr20-59817947-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.1328+11753G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,206 control chromosomes in the GnomAD database, including 1,933 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 0.14 (1933 hom., cov: 33)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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 (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR3	NM_080672.5	c.1328+11753G>T		intron_variant		ENST00000371015.6	NP_542403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR3	ENST00000371015.6	c.1328+11753G>T		intron_variant		1	NM_080672.5	ENSP00000360054.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21960 AN: 152088 Hom.: 1934 Cov.: 33

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.144 AC: 21952 AN: 152206 Hom.: 1933 Cov.: 33 AF XY: 0.143 AC XY: 10654 AN XY: 74414

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0766

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.177

Alfa AF: 0.187 Hom.: 4058

Bravo AF: 0.142

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.75

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: rs1182531; hg19: chr20-58393002;