14-94096847-T-C

Position:

• chr14-94096847-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393115.7(IFI27L1):​c.-91T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 1,181,144 control chromosomes in the GnomAD database, including 181,921 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 0.59 (27944 hom., cov: 32)
  • Exomes 𝑓: 0.53 (153977 hom.)
• Consequence: IFI27L1 ENST00000393115.7 5_prime_UTR
• Scores: Splicing: ADA: 0.00001172
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFI27L1	NM_206949.3	c.-51-40T>C		intron_variant		ENST00000555523.6
IFI27L1	NM_145249.3	c.-91T>C		5_prime_UTR_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFI27L1	ENST00000555523.6	c.-51-40T>C		intron_variant		2	NM_206949.3	P1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89900 AN: 151882 Hom.: 27911 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.566

GnomAD3 exomes AF: 0.597 AC: 116425 AN: 195072 Hom.: 36565 AF XY: 0.595 AC XY: 62186 AN XY: 104596

Gnomad AFR exome AF: 0.735

Gnomad AMR exome AF: 0.596

Gnomad ASJ exome AF: 0.543

Gnomad EAS exome AF: 0.957

Gnomad SAS exome AF: 0.708

Gnomad FIN exome AF: 0.612

Gnomad NFE exome AF: 0.486

Gnomad OTH exome AF: 0.542

GnomAD4 exome AF: 0.535 AC: 550519 AN: 1029144 Hom.: 153977 Cov.: 13 AF XY: 0.539 AC XY: 283879 AN XY: 526600

Gnomad4 AFR exome AF: 0.737

Gnomad4 AMR exome AF: 0.583

Gnomad4 ASJ exome AF: 0.549

Gnomad4 EAS exome AF: 0.923

Gnomad4 SAS exome AF: 0.707

Gnomad4 FIN exome AF: 0.608

Gnomad4 NFE exome AF: 0.481

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.592 AC: 89980 AN: 152000 Hom.: 27944 Cov.: 32 AF XY: 0.599 AC XY: 44508 AN XY: 74272

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.571

Alfa AF: 0.513 Hom.: 46650

Bravo AF: 0.592

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	14
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000012
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7157940; hg19: chr14-94563193;