rs1182532

Variant names:

• chr20-59818490-C-A
• rs1182532
• NM_080672.5:c.1328+12296C>A

Variant summary

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

The NM_080672.5(PHACTR3):​c.1328+12296C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,240 control chromosomes in the GnomAD database, including 1,207 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 0.11 (1207 hom., cov: 33)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHACTR3	NM_080672.5	MANE Select	c.1328+12296C>A		intron	N/A	NP_542403.1	Q96KR7-1
	PHACTR3	NM_001199505.1		c.1319+12296C>A		intron	N/A	NP_001186434.1	Q96KR7-4
	PHACTR3	NM_001199506.2		c.1205+12296C>A		intron	N/A	NP_001186435.1	Q96KR7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHACTR3	ENST00000371015.6	TSL:1 MANE Select	c.1328+12296C>A		intron	N/A	ENSP00000360054.1	Q96KR7-1
	PHACTR3	ENST00000395636.6	TSL:1	c.1205+12296C>A		intron	N/A	ENSP00000378998.2	Q96KR7-2
	PHACTR3	ENST00000361300.4	TSL:1	c.995+12296C>A		intron	N/A	ENSP00000354555.4	Q96KR7-3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16799 AN: 152122 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0568

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.110 AC: 16795 AN: 152240 Hom.: 1207 Cov.: 33 AF XY: 0.109 AC XY: 8122 AN XY: 74420

African (AFR) AF: 0.0266 AC: 1107 AN: 41556

American (AMR) AF: 0.134 AC: 2050 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3470

East Asian (EAS) AF: 0.0643 AC: 333 AN: 5182

South Asian (SAS) AF: 0.0575 AC: 277 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1594 AN: 10594

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.152 AC: 10308 AN: 68006

Other (OTH) AF: 0.131 AC: 278 AN: 2116

Alfa AF: 0.129 Hom.: 585

Bravo AF: 0.106

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.22
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: rs1182532; hg19: chr20-58393545;