rs6015561

Variant names:

• chr20-59716906-G-A
• rs6015561
• NM_080672.5:c.119-26201G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-59716906-G-A
• chr20-59716906-G-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.119-26201G>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
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.43 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.119-26201G>A		intron	N/A	NP_542403.1
	PHACTR3	NM_001199505.1		c.110-26201G>A		intron	N/A	NP_001186434.1
	PHACTR3	NM_001199506.2		c.-5-26201G>A		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.119-26201G>A		intron	N/A	ENSP00000360054.1
	PHACTR3	ENST00000359926.7	TSL:2	c.110-26201G>A		intron	N/A	ENSP00000353002.3
	PHACTR3	ENST00000355648.8	TSL:2	c.-5-26201G>A		intron	N/A	ENSP00000347866.4

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

African (AFR) AF: 0.200 AC: 8300 AN: 41480

American (AMR) AF: 0.361 AC: 5515 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3470

East Asian (EAS) AF: 0.100 AC: 518 AN: 5164

South Asian (SAS) AF: 0.289 AC: 1386 AN: 4800

European-Finnish (FIN) AF: 0.371 AC: 3922 AN: 10572

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29482 AN: 67956

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.406 Hom.: 22162

Bravo AF: 0.336

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.65
PhyloP100		-2.7
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: rs6015561; hg19: chr20-58291961;