rs4711939

Variant names:

• chr6-13222645-T-C
• rs4711939
• NM_030948.6:c.987-5171T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-13222645-T-C
• chr6-13222645-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.987-5171T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,118 control chromosomes in the GnomAD database, including 30,310 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 0.62 (30310 hom., cov: 33)
• Consequence: PHACTR1 NM_030948.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHACTR1	NM_030948.6	c.987-5171T>C		intron_variant	Intron 8 of 14	ENST00000332995.12	NP_112210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHACTR1	ENST00000332995.12	c.987-5171T>C		intron_variant	Intron 8 of 14	2	NM_030948.6	ENSP00000329880.8

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94487 AN: 152002 Hom.: 30287 Cov.: 33

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.622 AC: 94556 AN: 152118 Hom.: 30310 Cov.: 33 AF XY: 0.617 AC XY: 45927 AN XY: 74380

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.641

Alfa AF: 0.566 Hom.: 1849

Bravo AF: 0.624

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.090
DANN	Benign	0.84

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: rs4711939; hg19: chr6-13222877;