Genetic Variant ENSG00000268173:n.*2366T>C (chr19-18178088-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 ENST00000593731.1(ENSG00000268173):n.*2366T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 645,272 control chromosomes in the GnomAD database, including 18,100 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 0.25 ( 5136 hom., cov: 32)

Exomes 𝑓: 0.22 ( 12964 hom. )

Consequence

ENSG00000268173
ENST00000593731.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.988

Publications

23 publications found

Variant links:

Genes affected

ENSG00000268173 (HGNC:):

ENSG00000268173 links:

IFI30 (HGNC:5398): (IFI30 lysosomal thiol reductase) The protein encoded by this gene is a lysosomal thiol reductase that at low pH can reduce protein disulfide bonds. The enzyme is expressed constitutively in antigen-presenting cells and induced by gamma-interferon in other cell types. This enzyme has an important role in MHC class II-restricted antigen processing. [provided by RefSeq, Jul 2008]

IFI30 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFI30	NM_006332.5 link	c.*177T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000407280.4	NP_006323.2	P13284A0A024R7N7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000268173	ENST00000593731.1 link	n.*2366T>C	non_coding_transcript_exon_variant	Exon 25 of 25	2		ENSP00000471914.1
IFI30	ENST00000407280.4 link	c.*177T>C	3_prime_UTR_variant	Exon 7 of 7	1	NM_006332.5	ENSP00000384886.1	P13284
ENSG00000268173	ENST00000593731.1 link	n.*2366T>C	3_prime_UTR_variant	Exon 25 of 25	2		ENSP00000471914.1
IFI30	ENST00000600463.1 link	n.2087T>C	non_coding_transcript_exon_variant	Exon 5 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38677

AN:

151934

Hom.:

5116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.253

GnomAD4 exome

AF:

0.223

AC:

110064

AN:

493220

Hom.:

12964

Cov.:

AF XY:

0.218

AC XY:

57130

AN XY:

261760

show subpopulations

African (AFR)

AF:

0.323

AC:

4364

AN:

13504

American (AMR)

AF:

0.296

AC:

7088

AN:

23928

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

3924

AN:

15088

East Asian (EAS)

AF:

0.127

AC:

4000

AN:

31382

South Asian (SAS)

AF:

0.146

AC:

7172

AN:

49288

European-Finnish (FIN)

AF:

0.232

AC:

7870

AN:

33872

Middle Eastern (MID)

AF:

0.282

AC:

593

AN:

2102

European-Non Finnish (NFE)

AF:

0.231

AC:

68471

AN:

296482

Other (OTH)

AF:

0.239

AC:

6582

AN:

27574

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

4695

9390

14086

18781

23476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.255

AC:

38756

AN:

152052

Hom.:

5136

Cov.:

AF XY:

0.254

AC XY:

18880

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.318

AC:

13179

AN:

41434

American (AMR)

AF:

0.291

AC:

4440

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3472

East Asian (EAS)

AF:

0.147

AC:

759

AN:

5174

South Asian (SAS)

AF:

0.149

AC:

719

AN:

4822

European-Finnish (FIN)

AF:

0.225

AC:

2378

AN:

10570

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15669

AN:

68006

Other (OTH)

AF:

0.256

AC:

540

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1458

2915

4373

5830

7288

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.240

Hom.:

11156

Bravo

AF:

0.261

Asia WGS

AF:

0.173

AC:

600

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.60

(source)

DANN

Benign

0.25

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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