rs1150607

chr6-13186695-G-Achr6-13186695-G-T

Variant summary

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

The NM_030948.6(PHACTR1):c.664+4009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,228 control chromosomes in the GnomAD database, including 52,435 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 0.83 (52435 hom., cov: 32)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR1	NM_030948.6	c.664+4009G>A		intron_variant		ENST00000332995.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR1	ENST00000332995.12	c.664+4009G>A		intron_variant		2	NM_030948.6	P3

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125649 AN: 152110 Hom.: 52382 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.826 AC: 125757 AN: 152228 Hom.: 52435 Cov.: 32 AF XY: 0.820 AC XY: 61019 AN XY: 74408

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.817

Alfa AF: 0.787 Hom.: 14785

Bravo AF: 0.835

Asia WGS AF: 0.736 AC: 2561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.013
Dann	Benign	0.44

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: rs1150607; hg19: chr6-13186927;