rs7932127

Positions:

• chr11-7568365-T-C

Variant summary

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

The NM_003621.5(PPFIBP2):​c.279+2598T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,008 control chromosomes in the GnomAD database, including 10,128 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 0.34 (10128 hom., cov: 32)
• Consequence: PPFIBP2 NM_003621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

PPFIBP2 (HGNC:9250): (PPFIA binding protein 2) This gene encodes a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. The encoded protein is a beta liprin and plays a role in axon guidance and neuronal synapse development by recruiting LAR protein-tyrosine phosphatases to the plasma membrane. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

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 (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPFIBP2	NM_003621.5	c.279+2598T>C		intron_variant		ENST00000299492.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPFIBP2	ENST00000299492.9	c.279+2598T>C		intron_variant		1	NM_003621.5	P2
PPFIBP2	ENST00000524548.5	c.143+2598T>C		intron_variant		3
PPFIBP2	ENST00000527790.5	c.279+2598T>C		intron_variant		3
PPFIBP2	ENST00000684123.1	c.279+2598T>C		intron_variant				A1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51866 AN: 151890 Hom.: 10104 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.342 AC: 51931 AN: 152008 Hom.: 10128 Cov.: 32 AF XY: 0.336 AC XY: 24967 AN XY: 74290

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.333

Alfa AF: 0.334 Hom.: 1804

Bravo AF: 0.349

Asia WGS AF: 0.318 AC: 1106 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	2.3
DANN	Benign	0.52

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: rs7932127; hg19: chr11-7589596;