chr6-13220090-C-T

Position:

• chr6-13220090-C-T

Variant summary

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

The NM_030948.6(PHACTR1):​c.987-7726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,076 control chromosomes in the GnomAD database, including 26,163 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 0.57 (26163 hom., cov: 32)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR1	NM_030948.6	c.987-7726C>T		intron_variant		ENST00000332995.12	NP_112210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR1	ENST00000332995.12	c.987-7726C>T		intron_variant		2	NM_030948.6	ENSP00000329880	P3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86748 AN: 151958 Hom.: 26141 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.571 AC: 86816 AN: 152076 Hom.: 26163 Cov.: 32 AF XY: 0.569 AC XY: 42277 AN XY: 74328

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.599

Alfa AF: 0.628 Hom.: 14124

Bravo AF: 0.572

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
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: rs4715167; hg19: chr6-13220322;