Variant chr14-94115784-T-TGGCCATGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM4BP6_Moderate

The ENST00000621160.5(IFI27):c.129_137dup(p.Met44_Ala46dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: not found (cov: 0)

Consequence

IFI27
ENST00000621160.5 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.306

Variant links:

Genes affected

IFI27 (HGNC:5397): (interferon alpha inducible protein 27) Enables RNA polymerase II-specific DNA-binding transcription factor binding activity; identical protein binding activity; and lamin binding activity. Involved in several processes, including cellular protein metabolic process; defense response to other organism; and extrinsic apoptotic signaling pathway. Acts upstream of or within negative regulation of transcription by RNA polymerase II and regulation of protein export from nucleus. Located in mitochondrial membrane and nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

IFI27 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in ENST00000621160.5.

BP6

Variant 14-94115784-T-TGGCCATGGC is Benign according to our data. Variant chr14-94115784-T-TGGCCATGGC is described in ClinVar as [Benign]. Clinvar id is 768677.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFI27	NM_001130080.3 linkuse as main transcript	c.129_137dup	p.Met44_Ala46dup	inframe_insertion	4/5	ENST00000621160.5
IFI27	XM_047431346.1 linkuse as main transcript	c.160_168dup	p.His54_Gly56dup	inframe_insertion	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFI27	ENST00000621160.5 linkuse as main transcript	c.129_137dup	p.Met44_Ala46dup	inframe_insertion	4/5	1	NM_001130080.3	P2	P40305-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.602

AC:

134145

AN:

222672

Hom.:

41079

AF XY:

0.604

AC XY:

72898

AN XY:

120598

show subpopulations

Gnomad AFR exome

AF:

0.781

Gnomad AMR exome

AF:

0.551

Gnomad ASJ exome

AF:

0.702

Gnomad EAS exome

AF:

0.583

Gnomad SAS exome

AF:

0.648

Gnomad FIN exome

AF:

0.490

Gnomad NFE exome

AF:

0.595

Gnomad OTH exome

AF:

0.637

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Asia WGS

AF:

0.635

AC:

2210

AN:

3478

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

Dec 31, 2019

- -

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