11-7535346-A-G

Variant names:

• chr11-7535346-A-G
• rs12791447
• NM_003621.5:c.-36-14094A>G

Variant summary

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

The NM_003621.5(PPFIBP2):​c.-36-14094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,290 control chromosomes in the GnomAD database, including 518 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 0.068 (518 hom., cov: 33)
• Consequence: PPFIBP2 NM_003621.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

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]

LOC124902806 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPFIBP2	NM_003621.5	c.-36-14094A>G		intron_variant	Intron 1 of 23	ENST00000299492.9	NP_003612.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPFIBP2	ENST00000299492.9	c.-36-14094A>G		intron_variant	Intron 1 of 23	1	NM_003621.5	ENSP00000299492.4
PPFIBP2	ENST00000684123.1	c.-36-14094A>G		intron_variant	Intron 1 of 26			ENSP00000507842.1
PPFIBP2	ENST00000526873.5	c.-36-14094A>G		intron_variant	Intron 1 of 2	4		ENSP00000434641.1
PPFIBP2	ENST00000528947.5	c.-192-12998A>G		intron_variant	Intron 1 of 3	2		ENSP00000431724.1

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10413 AN: 152172 Hom.: 512 Cov.: 33

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0685 AC: 10427 AN: 152290 Hom.: 518 Cov.: 33 AF XY: 0.0721 AC XY: 5371 AN XY: 74474

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.0661

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.0733 Hom.: 687

Bravo AF: 0.0715

Asia WGS AF: 0.125 AC: 435 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	0.41
DANN	Benign	0.29

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: rs12791447; hg19: chr11-7556577;