rs1150607

Variant names:

• chr6-13186695-G-A
• rs1150607
• NM_030948.6:c.664+4009G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-13186695-G-A
• chr6-13186695-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

PHACTR1 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 70

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• infantile spasms

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHACTR1	NM_030948.6	c.664+4009G>A		intron_variant	Intron 7 of 14	ENST00000332995.12	NP_112210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHACTR1	ENST00000332995.12	c.664+4009G>A		intron_variant	Intron 7 of 14	2	NM_030948.6	ENSP00000329880.8

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

African (AFR) AF: 0.930 AC: 38660 AN: 41548

American (AMR) AF: 0.772 AC: 11805 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2477 AN: 3472

East Asian (EAS) AF: 0.935 AC: 4837 AN: 5174

South Asian (SAS) AF: 0.553 AC: 2669 AN: 4824

European-Finnish (FIN) AF: 0.798 AC: 8446 AN: 10588

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54117 AN: 68014

Other (OTH) AF: 0.817 AC: 1727 AN: 2114

Alfa AF: 0.795 Hom.: 21748

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
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1150607; hg19: chr6-13186927;