chr20-59640082-A-G

Position:

• chr20-59640082-A-G

Variant summary

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

The ENST00000371015.6(PHACTR3):​c.118+34950A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,098 control chromosomes in the GnomAD database, including 39,502 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 0.72 (39502 hom., cov: 33)
• Consequence: PHACTR3 ENST00000371015.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR3	NM_080672.5	c.118+34950A>G		intron_variant		ENST00000371015.6	NP_542403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR3	ENST00000371015.6	c.118+34950A>G		intron_variant		1	NM_080672.5	ENSP00000360054	A1
PHACTR3	ENST00000359926.7	c.109+62465A>G		intron_variant		2		ENSP00000353002
PHACTR3	ENST00000434923.1	c.118+34950A>G		intron_variant		5		ENSP00000390915
PHACTR3	ENST00000541461.5	c.-6+11266A>G		intron_variant		2		ENSP00000442483	P4

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109353 AN: 151980 Hom.: 39495 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.719 AC: 109407 AN: 152098 Hom.: 39502 Cov.: 33 AF XY: 0.722 AC XY: 53674 AN XY: 74348

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.713

Alfa AF: 0.662 Hom.: 4138

Bravo AF: 0.715

Asia WGS AF: 0.792 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.54

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: rs6064822; hg19: chr20-58215137;