chr20-59692593-G-T

Variant names:

• chr20-59692593-G-T
• rs6100556
• NM_080672.5:c.119-50514G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080672.5(PHACTR3):​c.119-50514G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,008 control chromosomes in the GnomAD database, including 20,126 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 0.50 (20126 hom., cov: 32)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHACTR3	NM_080672.5	c.119-50514G>T		intron_variant	Intron 1 of 12	ENST00000371015.6	NP_542403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHACTR3	ENST00000371015.6	c.119-50514G>T		intron_variant	Intron 1 of 12	1	NM_080672.5	ENSP00000360054.1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75638 AN: 151890 Hom.: 20062 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.499 AC: 75777 AN: 152008 Hom.: 20126 Cov.: 32 AF XY: 0.498 AC XY: 36990 AN XY: 74288

African (AFR) AF: 0.694 AC: 28765 AN: 41460

American (AMR) AF: 0.431 AC: 6584 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3148 AN: 5164

South Asian (SAS) AF: 0.434 AC: 2087 AN: 4810

European-Finnish (FIN) AF: 0.457 AC: 4815 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27700 AN: 67968

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.432 Hom.: 40411

Bravo AF: 0.506

Asia WGS AF: 0.535 AC: 1858 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	3.2
DANN	Benign	0.47
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6100556; hg19: chr20-58267648;