rs552282

Variant names:

• chr11-70383065-G-A
• rs552282
• ENST00000526262.5:n.*2036G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526262.5(PPFIA1):​n.*2036G>A 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 0.376 in 409,048 control chromosomes in the GnomAD database, including 31,813 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 0.43 (16041 hom., cov: 33)
  • Exomes 𝑓: 0.34 (15772 hom.)
• Consequence: PPFIA1 ENST00000526262.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 20 publications found

Genes affected

PPFIA1 (HGNC:9245): (PTPRF interacting protein alpha 1) 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. This protein binds to the intracellular membrane-distal phosphatase domain of tyrosine phosphatase LAR, and appears to localize LAR to cell focal adhesions. This interaction may regulate the disassembly of focal adhesion and thus help orchestrate cell-matrix interactions. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

CTTN-DT (HGNC:55592): (CTTN divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.009).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPFIA1	NM_003626.5	c.*75G>A		3_prime_UTR_variant	Exon 28 of 28	ENST00000253925.12	NP_003617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPFIA1	ENST00000253925.12	c.*75G>A		3_prime_UTR_variant	Exon 28 of 28	1	NM_003626.5	ENSP00000253925.7

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65920 AN: 151828 Hom.: 16016 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.419

GnomAD2 exomes AF: 0.335 AC: 30305 AN: 90372 AF XY: 0.331

Gnomad AFR exome AF: 0.634

Gnomad AMR exome AF: 0.419

Gnomad ASJ exome AF: 0.291

Gnomad EAS exome AF: 0.106

Gnomad FIN exome AF: 0.403

Gnomad NFE exome AF: 0.327

Gnomad OTH exome AF: 0.346

GnomAD4 exome AF: 0.341 AC: 87654 AN: 257102 Hom.: 15772 Cov.: 0 AF XY: 0.338 AC XY: 50500 AN XY: 149396

African (AFR) AF: 0.614 AC: 2912 AN: 4744

American (AMR) AF: 0.421 AC: 5947 AN: 14114

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 2837 AN: 9624

East Asian (EAS) AF: 0.106 AC: 663 AN: 6232

South Asian (SAS) AF: 0.334 AC: 16961 AN: 50810

European-Finnish (FIN) AF: 0.400 AC: 4982 AN: 12444

Middle Eastern (MID) AF: 0.337 AC: 904 AN: 2684

European-Non Finnish (NFE) AF: 0.335 AC: 48312 AN: 144228

Other (OTH) AF: 0.338 AC: 4136 AN: 12222

GnomAD4 genome AF: 0.434 AC: 65999 AN: 151946 Hom.: 16041 Cov.: 33 AF XY: 0.433 AC XY: 32181 AN XY: 74266

African (AFR) AF: 0.650 AC: 26949 AN: 41482

American (AMR) AF: 0.431 AC: 6571 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3470

East Asian (EAS) AF: 0.121 AC: 624 AN: 5156

South Asian (SAS) AF: 0.335 AC: 1607 AN: 4796

European-Finnish (FIN) AF: 0.412 AC: 4334 AN: 10528

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23529 AN: 67956

Other (OTH) AF: 0.419 AC: 885 AN: 2110

Alfa AF: 0.392 Hom.: 20160

Bravo AF: 0.443

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.94
PhyloP100		-0.39
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs552282; hg19: chr11-70229171;