rs10776724

chr1-111326865-C-A

Variant summary

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

The XM_005270472.2(PIFO):c.169+1982C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,950 control chromosomes in the GnomAD database, including 18,074 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 0.48 (18074 hom., cov: 32)
• Consequence: PIFO XM_005270472.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

PIFO (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIFO	XM_005270472.2	c.169+1982C>A		intron_variant
PIFO	XM_017000322.2	c.169+1982C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73496 AN: 151832 Hom.: 18062 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.484 AC: 73552 AN: 151950 Hom.: 18074 Cov.: 32 AF XY: 0.482 AC XY: 35777 AN XY: 74274

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.471

Alfa AF: 0.509 Hom.: 38294

Bravo AF: 0.470

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.22
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10776724; hg19: chr1-111869487;