rs2148809

Positions:

• chr20-59788816-A-G

Variant summary

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

The NM_080672.5(PHACTR3):​c.1174+14326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,102 control chromosomes in the GnomAD database, including 1,253 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 0.084 (1253 hom., cov: 33)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR3	NM_080672.5	c.1174+14326A>G		intron_variant		ENST00000371015.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR3	ENST00000371015.6	c.1174+14326A>G		intron_variant		1	NM_080672.5	A1

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12794 AN: 151984 Hom.: 1253 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.00405

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0842 AC: 12801 AN: 152102 Hom.: 1253 Cov.: 33 AF XY: 0.0836 AC XY: 6218 AN XY: 74346

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0370

Gnomad4 FIN AF: 0.00405

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0539 Hom.: 113

Bravo AF: 0.0987

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.69

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: rs2148809; hg19: chr20-58363871;