rs17089814

chr13-72865834-T-A

Variant summary

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

The NM_006346.4(PIBF1):c.1322+11679T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,192 control chromosomes in the GnomAD database, including 2,301 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 0.10 (2301 hom., cov: 32)
• Consequence: PIBF1 NM_006346.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77

Genes affected

PIBF1 (HGNC:23352): (progesterone immunomodulatory binding factor 1) This gene encodes a protein that is induced by the steroid hormone progesterone and plays a role in the maintenance of pregnancy. The encoded protein regulates multiple facets of the immune system to promote normal pregnancy including cytokine synthesis, natural killer (NK) cell activity, and arachidonic acid metabolism. Low serum levels of this protein have been associated with spontaneous pre-term labor in humans. This protein may promote the proliferation, migration and invasion of glioma. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIBF1	NM_006346.4	c.1322+11679T>A		intron_variant		ENST00000326291.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIBF1	ENST00000326291.11	c.1322+11679T>A		intron_variant		1	NM_006346.4	P1
PIBF1	ENST00000615625.1	c.-136+30466T>A		intron_variant		1
PIBF1	ENST00000617689.4	c.1322+11679T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15652 AN: 152074 Hom.: 2292 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.103 AC: 15683 AN: 152192 Hom.: 2301 Cov.: 32 AF XY: 0.0998 AC XY: 7426 AN XY: 74434

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0406

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0109

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0675 Hom.: 162

Bravo AF: 0.115

Asia WGS AF: 0.0480 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	12
Dann	Benign	0.74

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: rs17089814; hg19: chr13-73439972;