rs12426725

Positions:

• chr12-81449349-G-A

Variant summary

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

The NM_003625.5(PPFIA2):​c.406-3629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,970 control chromosomes in the GnomAD database, including 2,917 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 (2917 hom., cov: 32)
• Consequence: PPFIA2 NM_003625.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

PPFIA2 (HGNC:9246): (PTPRF interacting protein alpha 2) The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. It has been proposed that liprins are multivalent proteins that form complex structures and act as scaffolds for the recruitment and anchoring of LAR family of tyrosine phosphatases. This protein has been shown to bind the calcium/calmodulin-dependent serine protein kinase (MAGUK family) protein (also known as CASK) and proposed to regulate higher-order brain functions in mammals. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPFIA2	NM_003625.5	c.406-3629C>T		intron_variant		ENST00000549396.6	NP_003616.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPFIA2	ENST00000549396.6	c.406-3629C>T		intron_variant		1	NM_003625.5	ENSP00000450337	A1
	ENST00000671127.1	n.205-15890G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28221 AN: 151852 Hom.: 2907 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.186 AC: 28260 AN: 151970 Hom.: 2917 Cov.: 32 AF XY: 0.187 AC XY: 13920 AN XY: 74286

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0445

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.196

Alfa AF: 0.158 Hom.: 2333

Bravo AF: 0.188

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.20

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: rs12426725; hg19: chr12-81843128;