chr20-59788816-A-G

Variant names:

• chr20-59788816-A-G
• rs2148809
• NM_080672.5:c.1174+14326A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080672.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHACTR3	NM_080672.5	MANE Select	c.1174+14326A>G		intron	N/A	NP_542403.1
	PHACTR3	NM_001199505.1		c.1165+14326A>G		intron	N/A	NP_001186434.1
	PHACTR3	NM_001199506.2		c.1051+14326A>G		intron	N/A	NP_001186435.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHACTR3	ENST00000371015.6	TSL:1 MANE Select	c.1174+14326A>G		intron	N/A	ENSP00000360054.1
	PHACTR3	ENST00000395636.6	TSL:1	c.1051+14326A>G		intron	N/A	ENSP00000378998.2
	PHACTR3	ENST00000361300.4	TSL:1	c.841+14326A>G		intron	N/A	ENSP00000354555.4

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

African (AFR) AF: 0.233 AC: 9664 AN: 41462

American (AMR) AF: 0.0606 AC: 927 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3468

East Asian (EAS) AF: 0.191 AC: 982 AN: 5144

South Asian (SAS) AF: 0.0370 AC: 178 AN: 4816

European-Finnish (FIN) AF: 0.00405 AC: 43 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 736 AN: 68002

Other (OTH) AF: 0.0739 AC: 156 AN: 2112

Alfa AF: 0.0609 Hom.: 136

Bravo AF: 0.0987

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2148809; hg19: chr20-58363871;