rs3737880

Positions:

• chr1-203077547-G-C

Variant summary

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

The NM_001304331.2(PPFIA4):​c.*1157G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,160 control chromosomes in the GnomAD database, including 1,689 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 0.13 (1688 hom., cov: 32)
  • Exomes 𝑓: 0.56 (1 hom.)
• Consequence: PPFIA4 NM_001304331.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

PPFIA4 (HGNC:9248): (PTPRF interacting protein alpha 4) PPFIA4, or liprin-alpha-4, belongs to the liprin-alpha gene family. See liprin-alpha-1 (LIP1, or PPFIA1; MIM 611054) for background on liprins.[supplied by OMIM, Mar 2008]

PPFIA4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPFIA4	NM_001304331.2	c.*1157G>C		3_prime_UTR_variant	30/30	ENST00000295706.9	NP_001291260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPFIA4	ENST00000295706.9	c.*1157G>C		3_prime_UTR_variant	30/30	5	NM_001304331.2	ENSP00000295706.5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19978 AN: 152026 Hom.: 1689 Cov.: 32

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0819

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.563 AC: 9 AN: 16 Hom.: 1 Cov.: 0 AF XY: 0.583 AC XY: 7 AN XY: 12

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.131 AC: 19988 AN: 152144 Hom.: 1688 Cov.: 32 AF XY: 0.135 AC XY: 10017 AN XY: 74368

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0821

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.138

Alfa AF: 0.145 Hom.: 239

Bravo AF: 0.123

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.40
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3737880; hg19: chr1-203046675;