rs6026990

Positions:

• chr20-59602560-T-A

Variant summary

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

The NM_001199505.1(PHACTR3):​c.109+24943T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,854 control chromosomes in the GnomAD database, including 3,046 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 0.16 (3046 hom., cov: 32)
• Consequence: PHACTR3 NM_001199505.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

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 = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR3	NM_001199505.1	c.109+24943T>A		intron_variant
PHACTR3	XM_011528525.3	c.-6+18872T>A		intron_variant
PHACTR3	XM_017027626.3	c.-6+23107T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR3	ENST00000359926.7	c.109+24943T>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23959 AN: 151740 Hom.: 3025 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0629

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.158 AC: 24016 AN: 151854 Hom.: 3046 Cov.: 32 AF XY: 0.159 AC XY: 11766 AN XY: 74182

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0629

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0912 Hom.: 620

Bravo AF: 0.173

Asia WGS AF: 0.240 AC: 833 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	0.56
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6026990; hg19: chr20-58177615;