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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFI27L1	NM_206949.3 link	c.-51-40T>C		intron_variant	Intron 1 of 4	ENST00000555523.6	NP_996832.1
IFI27L1	NM_145249.3 link	c.-91T>C		5_prime_UTR_variant	Exon 2 of 5		NP_660292.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFI27L1	ENST00000555523.6 link	c.-51-40T>C		intron_variant	Intron 1 of 4	2	NM_206949.3	ENSP00000451851.1

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over