Variant rs1131692160 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_006346.4(PIBF1):c.1151_1152insGCTTCGCAGATTGAAAACCAACCAAGAAATTGATCA(p.Ile384delinsMetLeuArgArgLeuLysThrAsnGlnGluIleAspHis) variant causes a protein altering change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

PIBF1
NM_006346.4 protein_altering

Scores

Not classified

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.250

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_006346.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIBF1	NM_006346.4 linkuse as main transcript	c.1151_1152insGCTTCGCAGATTGAAAACCAACCAAGAAATTGATCA	p.Ile384delinsMetLeuArgArgLeuLysThrAsnGlnGluIleAspHis	protein_altering_variant	9/18	ENST00000326291.11	NP_006337.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIBF1	ENST00000326291.11 linkuse as main transcript	c.1151_1152insGCTTCGCAGATTGAAAACCAACCAAGAAATTGATCA	p.Ile384delinsMetLeuArgArgLeuLysThrAsnGlnGluIleAspHis	protein_altering_variant	9/18	1	NM_006346.4	ENSP00000317144	P1	Q8WXW3-1
PIBF1	ENST00000617689.4 linkuse as main transcript	c.1151_1152insGCTTCGCAGATTGAAAACCAACCAAGAAATTGATCA	p.Ile384delinsMetLeuArgArgLeuLysThrAsnGlnGluIleAspHis	protein_altering_variant	9/16	1		ENSP00000478697
PIBF1	ENST00000615625.1 linkuse as main transcript	c.-208_-207insGCTTCGCAGATTGAAAACCAACCAAGAAATTGATCA		5_prime_UTR_variant	2/9	1		ENSP00000483286		Q8WXW3-2
PIBF1	ENST00000492803.1 linkuse as main transcript			downstream_gene_variant		3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Familial aplasia of the vermis

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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