rs6015561

Positions:

• chr20-59716906-G-A
• chr20-59716906-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.119-26201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,026 control chromosomes in the GnomAD database, including 9,814 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 0.34 (9814 hom., cov: 32)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR3	NM_080672.5	c.119-26201G>A		intron_variant		ENST00000371015.6	NP_542403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR3	ENST00000371015.6	c.119-26201G>A		intron_variant		1	NM_080672.5	ENSP00000360054	A1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52066 AN: 151908 Hom.: 9820 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.342 AC: 52058 AN: 152026 Hom.: 9814 Cov.: 32 AF XY: 0.336 AC XY: 25004 AN XY: 74308

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.367

Alfa AF: 0.415 Hom.: 14149

Bravo AF: 0.336

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.65

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: rs6015561; hg19: chr20-58291961;