Variant 13-72792566-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006346.4(PIBF1):c.353+19A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,074,314 control chromosomes in the GnomAD database, including 56,465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.31 ( 7989 hom., cov: 30)

Exomes 𝑓: 0.33 ( 48476 hom. )

Consequence

PIBF1
NM_006346.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.581

Variant links:

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]

PIBF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 13-72792566-A-T is Benign according to our data. Variant chr13-72792566-A-T is described in ClinVar as [Benign]. Clinvar id is 1530576.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIBF1	NM_006346.4 linkuse as main transcript	c.353+19A>T		intron_variant		ENST00000326291.11

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
PIBF1	ENST00000326291.11 linkuse as main transcript	c.353+19A>T	intron_variant	1	NM_006346.4	P1	Q8WXW3-1
PIBF1	ENST00000615625.1 linkuse as main transcript	c.-262+10217A>T	intron_variant	1			Q8WXW3-2
PIBF1	ENST00000617689.4 linkuse as main transcript	c.353+19A>T	intron_variant	1
PIBF1	ENST00000489797.1 linkuse as main transcript	n.297+19A>T	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

45713

AN:

149726

Hom.:

7979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.469

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.318

GnomAD3 exomes

AF:

0.398

AC:

59166

AN:

148832

Hom.:

10046

AF XY:

0.402

AC XY:

33107

AN XY:

82402

show subpopulations

Gnomad AFR exome

AF:

0.162

Gnomad AMR exome

AF:

0.591

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.474

Gnomad SAS exome

AF:

0.510

Gnomad FIN exome

AF:

0.360

Gnomad NFE exome

AF:

0.369

Gnomad OTH exome

AF:

0.405

GnomAD4 exome

AF:

0.328

AC:

303595

AN:

924478

Hom.:

48476

Cov.:

AF XY:

0.334

AC XY:

158388

AN XY:

474544

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.540

Gnomad4 ASJ exome

AF:

0.264

Gnomad4 EAS exome

AF:

0.498

Gnomad4 SAS exome

AF:

0.451

Gnomad4 FIN exome

AF:

0.325

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.305

AC:

45755

AN:

149836

Hom.:

7989

Cov.:

AF XY:

0.314

AC XY:

22962

AN XY:

73116

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.455

Gnomad4 ASJ

AF:

0.266

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.500

Gnomad4 FIN

AF:

0.341

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.317

Alfa

AF:

0.310

Hom.:

984

Bravo

AF:

0.305

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.26

DANN

Benign

0.21

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over