ENST00000393115.7:c.-91T>A

Variant names:

• chr14-94096847-T-A
• rs7157940
• ENST00000393115.7:c.-91T>A

Variant summary

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

The ENST00000393115.7(IFI27L1):​c.-91T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IFI27L1 ENST00000393115.7 5_prime_UTR
• Scores: Splicing: ADA: 0.00001815
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 29 publications found

Genes affected

IFI27L1 (HGNC:19754): (interferon alpha inducible protein 27 like 1) Involved in apoptotic process. Predicted to be integral component of membrane. Predicted to be active in mitochondrion. [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=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000393115.7. 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
	IFI27L1	NM_206949.3	MANE Select	c.-51-40T>A		intron	N/A	NP_996832.1	Q96BM0
	IFI27L1	NM_145249.3		c.-91T>A		5_prime_UTR	Exon 2 of 5	NP_660292.1	Q96BM0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFI27L1	ENST00000393115.7	TSL:1	c.-91T>A		5_prime_UTR	Exon 2 of 5	ENSP00000376824.3	Q96BM0
	IFI27L1	ENST00000555523.6	TSL:2 MANE Select	c.-51-40T>A		intron	N/A	ENSP00000451851.1	Q96BM0
	IFI27L1	ENST00000929345.1		c.-91T>A		5_prime_UTR	Exon 2 of 4	ENSP00000599404.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1031816 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 527926

African (AFR) AF: 0.00 AC: 0 AN: 25558

American (AMR) AF: 0.00 AC: 0 AN: 37986

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22840

East Asian (EAS) AF: 0.00 AC: 0 AN: 36490

South Asian (SAS) AF: 0.00 AC: 0 AN: 73952

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51266

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4994

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 732532

Other (OTH) AF: 0.00 AC: 0 AN: 46198

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	16
DANN	Benign	0.41
PhyloP100		-0.99
PromoterAI		0.0051	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000018
dbscSNV1_RF	Benign	0.020
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.20		Position offset: -41

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

dbSNP: rs7157940;

hg19: chr14-94563193;