chr14-94116589-C-A

Variant names:

• chr14-94116589-C-A
• rs2799
• NM_001130080.3:c.*62C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001130080.3(IFI27):​c.*62C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000841 in 1,189,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 8.4e-7 (0 hom.)
• Consequence: IFI27 NM_001130080.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 12 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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.*62C>A		3_prime_UTR	Exon 5 of 5	NP_001123552.1	P40305-2
	IFI27	NM_001288952.2		c.*62C>A		3_prime_UTR	Exon 6 of 6	NP_001275881.1	P40305-2
	IFI27	NM_001288956.2		c.*62C>A		3_prime_UTR	Exon 5 of 5	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.*62C>A		3_prime_UTR	Exon 5 of 5	ENSP00000483498.1	P40305-2
	IFI27	ENST00000612813.4	TSL:3	c.*62C>A		3_prime_UTR	Exon 5 of 5	ENSP00000483430.1	P40305-2
	IFI27	ENST00000616764.5	TSL:2	c.*62C>A		3_prime_UTR	Exon 6 of 6	ENSP00000477753.1	P40305-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 8.41e-7 AC: 1 AN: 1189092 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 599062

African (AFR) AF: 0.00 AC: 0 AN: 27876

American (AMR) AF: 0.00 AC: 0 AN: 37322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23880

East Asian (EAS) AF: 0.0000270 AC: 1 AN: 36976

South Asian (SAS) AF: 0.00 AC: 0 AN: 76738

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50244

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5300

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 879578

Other (OTH) AF: 0.00 AC: 0 AN: 51178

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 13

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		0.97

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

Other links and lift over

dbSNP: rs2799; hg19: chr14-94582926;