rs6027005

Variant names:

• chr20-59624163-C-T
• rs6027005
• NM_080672.5:c.118+19031C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_080672.5(PHACTR3):​c.118+19031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0375 in 152,070 control chromosomes in the GnomAD database, including 122 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 0.038 (122 hom., cov: 32)
• Consequence: PHACTR3 NM_080672.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.99).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0375 (5707/152070) while in subpopulation AFR AF= 0.0421 (1746/41482). AF 95% confidence interval is 0.0406. There are 122 homozygotes in gnomad4. There are 2651 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 5707 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHACTR3	NM_080672.5	c.118+19031C>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.118+19031C>T		intron_variant	Intron 1 of 12	1	NM_080672.5	ENSP00000360054.1
PHACTR3	ENST00000359926.7	c.109+46546C>T		intron_variant	Intron 1 of 12	2		ENSP00000353002.3
PHACTR3	ENST00000434923.1	c.118+19031C>T		intron_variant	Intron 3 of 3	5		ENSP00000390915.1

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5706 AN: 151950 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0375 AC: 5707 AN: 152070 Hom.: 122 Cov.: 32 AF XY: 0.0357 AC XY: 2651 AN XY: 74344

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.0288

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0458 Hom.: 34

Bravo AF: 0.0381

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6027005; hg19: chr20-58199218;