rs7768030

chr6-12822741-A-Cchr6-12822741-A-T

Variant summary

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

The NM_030948.6(PHACTR1):c.250+72951A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,148 control chromosomes in the GnomAD database, including 1,303 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 0.12 (1303 hom., cov: 32)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHACTR1	NM_030948.6	c.250+72951A>C		intron_variant		ENST00000332995.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHACTR1	ENST00000332995.12	c.250+72951A>C		intron_variant		2	NM_030948.6	P3

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18316 AN: 152030 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.121 AC: 18364 AN: 152148 Hom.: 1303 Cov.: 32 AF XY: 0.121 AC XY: 9006 AN XY: 74390

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0591

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0878

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0839 Hom.: 819

Bravo AF: 0.129

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	7.0
Dann	Benign	0.33

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: rs7768030; hg19: chr6-12822973;