chr19-18178088-T-C

Position:

• chr19-18178088-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006332.5(IFI30):​c.*177T>C variant causes a 3 prime UTR 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: IFI30 NM_006332.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

Genes affected

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
IFI30	NM_006332.5	c.*177T>C		3_prime_UTR_variant	7/7	ENST00000407280.4	NP_006323.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFI30	ENST00000407280.4	c.*177T>C		3_prime_UTR_variant	7/7	1	NM_006332.5	ENSP00000384886	P1
IFI30	ENST00000600463.1	n.2087T>C		non_coding_transcript_exon_variant	5/5	2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38677 AN: 151934 Hom.: 5116 Cov.: 32

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.: 5 AF XY: 0.218 AC XY: 57130 AN XY: 261760

Gnomad4 AFR exome AF: 0.323

Gnomad4 AMR exome AF: 0.296

Gnomad4 ASJ exome AF: 0.260

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.232

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.239

GnomAD4 genome AF: 0.255 AC: 38756 AN: 152052 Hom.: 5136 Cov.: 32 AF XY: 0.254 AC XY: 18880 AN XY: 74332

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.256

Alfa AF: 0.236 Hom.: 7602

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
DANN	Benign	0.25

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

LitVar

Other links and lift over

dbSNP: rs1045747; hg19: chr19-18288898; COSMIC: COSV69576667; COSMIC: COSV69576667;