rs10979

Positions:

• chr6-143568902-G-A

Variant summary

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

The NR_027113.2(PHACTR2-AS1):​n.438C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,796 control chromosomes in the GnomAD database, including 28,771 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 0.61 (28771 hom., cov: 32)
• Consequence: PHACTR2-AS1 NR_027113.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

PHACTR2-AS1 (HGNC:):

PHACTR2 (HGNC:20956): (phosphatase and actin regulator 2) Predicted to enable actin binding activity. Predicted to be involved in actin cytoskeleton organization. Predicted to be located in plasma membrane and platelet alpha granule membrane. Implicated in Parkinson's disease and multiple sclerosis. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHACTR2-AS1	NR_027113.2	n.438C>T		non_coding_transcript_exon_variant	1/3
PHACTR2	NM_001394736.1	c.217+31695G>A		intron_variant			NP_001381665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHACTR2	ENST00000367584.8	c.217+31695G>A		intron_variant		5		ENSP00000356556

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92863 AN: 151680 Hom.: 28746 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.612 AC: 92936 AN: 151796 Hom.: 28771 Cov.: 32 AF XY: 0.612 AC XY: 45357 AN XY: 74170

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.604

Alfa AF: 0.648 Hom.: 64915

Bravo AF: 0.599

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10979; hg19: chr6-143890039;