9-21140673-C-G

Position:

• chr9-21140673-C-G

Variant summary

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

The NM_002177.3(IFNW1):​c.*310G>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 0.315 in 173,356 control chromosomes in the GnomAD database, including 8,990 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 0.31 (7809 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1181 hom.)
• Consequence: IFNW1 NM_002177.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

IFNW1 (HGNC:5448): (interferon omega 1) The protein encoded by this gene is an interferon and possesses antiviral activity. The encoded protein binds to the interferon alpha/beta receptor but not to the interferon gamma receptor. This intronless gene has several pseudogenes spread throughout the genome. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNW1	NM_002177.3	c.*310G>C		3_prime_UTR_variant	1/1	ENST00000380229.4	NP_002168.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNW1	ENST00000380229.4	c.*310G>C		3_prime_UTR_variant	1/1	6	NM_002177.3	ENSP00000369578.2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47496 AN: 151638 Hom.: 7796 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.312

GnomAD4 exome AF: 0.327 AC: 7056 AN: 21600 Hom.: 1181 Cov.: 0 AF XY: 0.330 AC XY: 3696 AN XY: 11216

Gnomad4 AFR exome AF: 0.270

Gnomad4 AMR exome AF: 0.204

Gnomad4 ASJ exome AF: 0.312

Gnomad4 EAS exome AF: 0.176

Gnomad4 SAS exome AF: 0.315

Gnomad4 FIN exome AF: 0.383

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.321

GnomAD4 genome AF: 0.313 AC: 47542 AN: 151756 Hom.: 7809 Cov.: 32 AF XY: 0.313 AC XY: 23248 AN XY: 74166

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.311

Alfa AF: 0.319 Hom.: 997

Bravo AF: 0.296

Asia WGS AF: 0.285 AC: 986 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.83
DANN	Benign	0.62

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: rs10964859; hg19: chr9-21140672;