rs273265

Variant names:

• chr19-18173526-A-G
• rs273265
• ENST00000593731.1:n.*1399-278A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 9 publications found

Genes affected

ENSG00000268173 (HGNC:):

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268173	ENST00000593731.1	n.*1399-278A>G		intron_variant	Intron 18 of 24	2		ENSP00000471914.1
IFI30	ENST00000597802.2	c.-38-278A>G		intron_variant	Intron 1 of 2	3		ENSP00000470527.2

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38957 AN: 151752 Hom.: 5212 Cov.: 31

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

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

GnomAD4 genome AF: 0.257 AC: 39051 AN: 151870 Hom.: 5243 Cov.: 31 AF XY: 0.257 AC XY: 19056 AN XY: 74258

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: 64 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15632 AN: 67872

Other (OTH) AF: 0.260 AC: 548 AN: 2104

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.032
DANN	Benign	0.59
PhyloP100		-1.0
PromoterAI		-0.0038	Neutral

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

Other links and lift over

dbSNP: rs273265; hg19: chr19-18284336;