dbSNP rs273265: ENSG00000268173:n.*1399-278A>G (chr19-18173526-A-G) – 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.*1399-278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 299,368 control chromosomes in the GnomAD database, including 8,826 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 0.26 ( 5243 hom., cov: 31)

Exomes 𝑓: 0.21 ( 3583 hom. )

Consequence

ENSG00000268173
ENST00000593731.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.997

Publications

9 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

new If you want to explore the variant's impact on the transcript ENST00000593731.1, 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593731.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268173	ENST00000593731.1	TSL:2	n.*1399-278A>G		intron	N/A	ENSP00000471914.1
	IFI30	ENST00000597802.2	TSL:3	c.-38-278A>G		intron	N/A	ENSP00000470527.2	M0QZG3

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

38957

AN:

151752

Hom.:

5212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.258

GnomAD4 exome

AF:

0.209

AC:

30835

AN:

147498

Hom.:

3583

AF XY:

0.203

AC XY:

15788

AN XY:

77790

show subpopulations

African (AFR)

AF:

0.312

AC:

1180

AN:

3786

American (AMR)

AF:

0.266

AC:

1156

AN:

4338

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

1221

AN:

4900

East Asian (EAS)

AF:

0.121

AC:

998

AN:

8266

South Asian (SAS)

AF:

0.124

AC:

2081

AN:

16812

European-Finnish (FIN)

AF:

0.229

AC:

2223

AN:

9718

Middle Eastern (MID)

AF:

0.281

AC:

203

AN:

722

European-Non Finnish (NFE)

AF:

0.219

AC:

19667

AN:

89918

Other (OTH)

AF:

0.233

AC:

2106

AN:

9038

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1170

2340

3510

4680

5850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

122

244

366

488

610

<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:

0.257

AC:

39051

AN:

151870

Hom.:

5243

Cov.:

AF XY:

0.257

AC XY:

19056

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.325

AC:

13447

AN:

41432

American (AMR)

AF:

0.292

AC:

4465

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

868

AN:

3470

East Asian (EAS)

AF:

0.139

AC:

714

AN:

5142

South Asian (SAS)

AF:

0.150

AC:

721

AN:

4814

European-Finnish (FIN)

AF:

0.232

AC:

2452

AN:

10562

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15632

AN:

67872

Other (OTH)

AF:

0.260

AC:

548

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1490

2980

4470

5960

7450

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:

0.254

Hom.:

669

Bravo

AF:

0.263

Asia WGS

AF:

0.173

AC:

599

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.032

(source)

DANN

Benign

0.59

PhyloP100

-1.0

PromoterAI

-0.0038

Neutral

(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

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