rs9357503

Positions:

• chr6-12841753-T-A
• chr6-12841753-T-C
• chr6-12841753-T-G

Variant summary

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

The NM_030948.6(PHACTR1):​c.250+91963T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,100 control chromosomes in the GnomAD database, including 3,062 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 0.19 (3062 hom., cov: 32)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR1	NM_030948.6	c.250+91963T>A		intron_variant		ENST00000332995.12	NP_112210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR1	ENST00000332995.12	c.250+91963T>A		intron_variant		2	NM_030948.6	ENSP00000329880	P3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29172 AN: 151984 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.192 AC: 29238 AN: 152100 Hom.: 3062 Cov.: 32 AF XY: 0.193 AC XY: 14318 AN XY: 74352

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.180

Alfa AF: 0.169 Hom.: 300

Bravo AF: 0.201

Asia WGS AF: 0.215 AC: 746 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.22

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: rs9357503; hg19: chr6-12841985;