14-94115843-GCC-TCG

Variant names:

• chr14-94115843-GCC-TCG
• NM_001130080.3:c.184_186delGCCinsTCG
• IFI27 p.Ala62Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001130080.3(IFI27):​c.184_186delGCCinsTCG​(p.Ala62Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A62T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IFI27 NM_001130080.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130080.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI27	NM_001130080.3	MANE Select	c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	NP_001123552.1	P40305-2
	IFI27	NM_001288952.2		c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	NP_001275881.1	P40305-2
	IFI27	NM_001288956.2		c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	NP_001275885.1	P40305-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI27	ENST00000621160.5	TSL:1 MANE Select	c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	ENSP00000483498.1	P40305-2
	IFI27	ENST00000612813.4	TSL:3	c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	ENSP00000483430.1	P40305-2
	IFI27	ENST00000616764.5	TSL:2	c.184_186delGCCinsTCG	p.Ala62Ser	missense	N/A	ENSP00000477753.1	P40305-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr14-94582180;