13-72969927-G-A

Position:

• chr13-72969927-G-A

Variant summary

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

The NM_006346.4(PIBF1):​c.1965-3664G>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 152,030 control chromosomes in the GnomAD database, including 2,310 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 (2310 hom., cov: 32)
• Consequence: PIBF1 NM_006346.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIBF1	NM_006346.4	c.1965-3664G>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.1965-3664G>A		intron_variant		1	NM_006346.4	ENSP00000317144.6

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15681 AN: 151912 Hom.: 2301 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0672

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

GnomAD4 genome AF: 0.103 AC: 15713 AN: 152030 Hom.: 2310 Cov.: 32 AF XY: 0.100 AC XY: 7443 AN XY: 74320

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.0115

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0665

Alfa AF: 0.0251 Hom.: 304

Bravo AF: 0.115

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.37

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: rs10492653; hg19: chr13-73544065;