chr13-72785554-C-A

Position:

• chr13-72785554-C-A

Variant summary

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

The ENST00000326291.11(PIBF1):​c.252+1833C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,050 control chromosomes in the GnomAD database, including 27,330 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 0.59 (27330 hom., cov: 32)
• Consequence: PIBF1 ENST00000326291.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIBF1	NM_006346.4	c.252+1833C>A		intron_variant		ENST00000326291.11	NP_006337.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIBF1	ENST00000326291.11	c.252+1833C>A		intron_variant		1	NM_006346.4	ENSP00000317144	P1
PIBF1	ENST00000615625.1	c.-262+3205C>A		intron_variant		1		ENSP00000483286
PIBF1	ENST00000617689.4	c.252+1833C>A		intron_variant		1		ENSP00000478697
PIBF1	ENST00000489797.1	n.196+3205C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90059 AN: 151932 Hom.: 27307 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.593 AC: 90137 AN: 152050 Hom.: 27330 Cov.: 32 AF XY: 0.596 AC XY: 44260 AN XY: 74312

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.565

Alfa AF: 0.556 Hom.: 4741

Bravo AF: 0.609

Asia WGS AF: 0.712 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.54

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: rs7321718; hg19: chr13-73359692;