Genetic Variant ENST00000393115.7:c.-91T>C (chr14-94096847-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Publications

29 publications found

Variant links:

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]

IFI27L1 links:

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new If you want to explore the variant's impact on the transcript ENST00000393115.7, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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>C		intron	N/A	NP_996832.1	Q96BM0
	IFI27L1	NM_145249.3		c.-91T>C		5_prime_UTR	Exon 2 of 5	NP_660292.1	Q96BM0

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

89900

AN:

151882

Hom.:

27911

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.597

AC:

116425

AN:

195072

AF XY:

0.595

show subpopulations

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 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.:

AF XY:

0.539

AC XY:

283879

AN XY:

526600

show subpopulations

African (AFR)

AF:

0.737

AC:

18806

AN:

25532

American (AMR)

AF:

0.583

AC:

22101

AN:

37928

Ashkenazi Jewish (ASJ)

AF:

0.549

AC:

12527

AN:

22798

East Asian (EAS)

AF:

0.923

AC:

33670

AN:

36488

South Asian (SAS)

AF:

0.707

AC:

52230

AN:

73872

European-Finnish (FIN)

AF:

0.608

AC:

31162

AN:

51230

Middle Eastern (MID)

AF:

0.593

AC:

2960

AN:

4988

European-Non Finnish (NFE)

AF:

0.481

AC:

351082

AN:

730162

Other (OTH)

AF:

0.563

AC:

25981

AN:

46146

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

12126

24251

36377

48502

60628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8806

17612

26418

35224

44030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.592

AC:

89980

AN:

152000

Hom.:

27944

Cov.:

AF XY:

0.599

AC XY:

44508

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.731

AC:

30304

AN:

41452

American (AMR)

AF:

0.531

AC:

8107

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

1950

AN:

3470

East Asian (EAS)

AF:

0.948

AC:

4920

AN:

5190

South Asian (SAS)

AF:

0.706

AC:

3392

AN:

4806

European-Finnish (FIN)

AF:

0.617

AC:

6515

AN:

10552

Middle Eastern (MID)

AF:

0.558

AC:

164

AN:

294

European-Non Finnish (NFE)

AF:

0.485

AC:

32973

AN:

67946

Other (OTH)

AF:

0.571

AC:

1203

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1751

3502

5253

7004

8755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

752

1504

2256

3008

3760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.526

Hom.:

96089

Bravo

AF:

0.592

Asia WGS

AF:

0.811

AC:

2818

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

(source)

DANN

Benign

0.39

PhyloP100

-0.99

PromoterAI

0.055

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over