NM_003621.5:c.279+2598T>C

Variant names:

• chr11-7568365-T-C
• rs7932127
• NM_003621.5:c.279+2598T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003621.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPFIBP2	NM_003621.5	MANE Select	c.279+2598T>C		intron	N/A	NP_003612.3	Q8ND30-1
	PPFIBP2	NM_001351853.2		c.279+2598T>C		intron	N/A	NP_001338782.2
	PPFIBP2	NM_001351854.2		c.279+2598T>C		intron	N/A	NP_001338783.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPFIBP2	ENST00000299492.9	TSL:1 MANE Select	c.279+2598T>C		intron	N/A	ENSP00000299492.4	Q8ND30-1
	PPFIBP2	ENST00000684123.1		c.279+2598T>C		intron	N/A	ENSP00000507842.1	A0A804HKA2
	PPFIBP2	ENST00000857461.1		c.279+2598T>C		intron	N/A	ENSP00000527520.1

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

African (AFR) AF: 0.539 AC: 22311 AN: 41406

American (AMR) AF: 0.215 AC: 3291 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1308 AN: 5176

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4808

European-Finnish (FIN) AF: 0.245 AC: 2592 AN: 10564

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19148 AN: 67980

Other (OTH) AF: 0.333 AC: 701 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		-0.090
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: rs7932127; hg19: chr11-7589596;