rs12526453

chr6-12927312-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030948.6(PHACTR1):c.251-126053C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,046 control chromosomes in the GnomAD database, including 6,182 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 0.27 (6182 hom., cov: 33)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

PHACTR1 (HGNC:20990): (phosphatase and actin regulator 1) The protein encoded by this gene is a member of the phosphatase and actin regulator family of proteins. This family member can bind actin and regulate the reorganization of the actin cytoskeleton. It plays a role in tubule formation and in endothelial cell survival. Polymorphisms in this gene are associated with susceptibility to myocardial infarction, coronary artery disease and cervical artery dissection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR1	NM_030948.6	c.251-126053C>G		intron_variant		ENST00000332995.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR1	ENST00000332995.12	c.251-126053C>G		intron_variant		2	NM_030948.6	P3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40653 AN: 151928 Hom.: 6174 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.267 AC: 40667 AN: 152046 Hom.: 6182 Cov.: 33 AF XY: 0.263 AC XY: 19555 AN XY: 74328

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.298

Alfa AF: 0.296 Hom.: 919

Bravo AF: 0.269

Asia WGS AF: 0.107 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.54
Dann	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs12526453; hg19: chr6-12927544;