14-94105764-G-T

Variant names:

• chr14-94105764-G-T
• rs9323902
• ENST00000614204.4:c.-298-1G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000614204.4(IFI27):​c.-298-1G>T variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,058 control chromosomes in the GnomAD database, including 13,897 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 0.40 (13895 hom., cov: 32)
  • Exomes 𝑓: 0.27 (2 hom.)
• Consequence: IFI27 ENST00000614204.4 splice_acceptor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614204.4. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI27	ENST00000614204.4	TSL:5	c.-298-1G>T		splice_acceptor intron	N/A	ENSP00000479250.1	A0A087WV79

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60540 AN: 151914 Hom.: 13871 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.269 AC: 7 AN: 26 Hom.: 2 Cov.: 0 AF XY: 0.300 AC XY: 6 AN XY: 20

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.399 AC: 60621 AN: 152032 Hom.: 13895 Cov.: 32 AF XY: 0.401 AC XY: 29843 AN XY: 74330

African (AFR) AF: 0.628 AC: 26050 AN: 41456

American (AMR) AF: 0.298 AC: 4557 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3462

East Asian (EAS) AF: 0.454 AC: 2335 AN: 5144

South Asian (SAS) AF: 0.471 AC: 2275 AN: 4828

European-Finnish (FIN) AF: 0.352 AC: 3721 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19055 AN: 67986

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.326 Hom.: 6312

Bravo AF: 0.399

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.33
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs9323902; hg19: chr14-94572110;