dbSNP rs17089814: PIBF1:c.1322+11679T>A (chr13-72865834-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.77

Publications

1 publications found

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 Gene-Disease associations (from GenCC):

Joubert syndrome 33
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
ciliopathy
Inheritance: AR Classification: MODERATE Submitted by: ClinGen
Joubert syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

PIBF1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PIBF1	NM_006346.4 link	c.1322+11679T>A		intron_variant	Intron 10 of 17	ENST00000326291.11	NP_006337.2	Q8WXW3-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PIBF1	ENST00000326291.11 link	c.1322+11679T>A	intron_variant	Intron 10 of 17	1	NM_006346.4	ENSP00000317144.6	Q8WXW3-1
PIBF1	ENST00000617689.4 link	c.1322+11679T>A	intron_variant	Intron 10 of 15	1		ENSP00000478697.1	A0A087WUI6
PIBF1	ENST00000615625.1 link	c.-136+30466T>A	intron_variant	Intron 2 of 8	1		ENSP00000483286.1	Q8WXW3-2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15652

AN:

152074

Hom.:

2292

Cov.:

show subpopulations

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.:

AF XY:

0.0998

AC XY:

7426

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.329

AC:

13640

AN:

41466

American (AMR)

AF:

0.0406

AC:

620

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0199

AC:

AN:

3466

East Asian (EAS)

AF:

0.0216

AC:

112

AN:

5188

South Asian (SAS)

AF:

0.0317

AC:

153

AN:

4828

European-Finnish (FIN)

AF:

0.0109

AC:

116

AN:

10624

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0121

AC:

823

AN:

68022

Other (OTH)

AF:

0.0659

AC:

139

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

551

1102

1654

2205

2756

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.74

PhyloP100

2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over