9-21178518-A-T

Variant names:

• chr9-21178518-A-T
• rs1477479

Variant summary

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

The variant allele was found at a frequency of 0.213 in 154,630 control chromosomes in the GnomAD database, including 3,889 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 0.21 (3843 hom., cov: 32)
  • Exomes 𝑓: 0.16 (46 hom.)
• Consequence: IFNWP15 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

Genes affected

IFNWP15 (HGNC:5449): (interferon omega 1 pseudogene 15)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442022.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNWP15	ENST00000442022.2	TSL:6	n.*71T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32430 AN: 152040 Hom.: 3835 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.165 AC: 407 AN: 2472 Hom.: 46 AF XY: 0.162 AC XY: 220 AN XY: 1354

African (AFR) AF: 0.167 AC: 4 AN: 24

American (AMR) AF: 0.324 AC: 22 AN: 68

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 4 AN: 34

East Asian (EAS) AF: 0.324 AC: 11 AN: 34

South Asian (SAS) AF: 0.133 AC: 25 AN: 188

European-Finnish (FIN) AF: 0.166 AC: 69 AN: 416

Middle Eastern (MID) AF: 0.150 AC: 6 AN: 40

European-Non Finnish (NFE) AF: 0.155 AC: 235 AN: 1512

Other (OTH) AF: 0.199 AC: 31 AN: 156

GnomAD4 genome AF: 0.214 AC: 32489 AN: 152158 Hom.: 3843 Cov.: 32 AF XY: 0.214 AC XY: 15940 AN XY: 74388

African (AFR) AF: 0.265 AC: 11006 AN: 41498

American (AMR) AF: 0.253 AC: 3872 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2149 AN: 5184

South Asian (SAS) AF: 0.110 AC: 532 AN: 4816

European-Finnish (FIN) AF: 0.198 AC: 2094 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11549 AN: 68006

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.201 Hom.: 384

Bravo AF: 0.223

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.30
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1477479; hg19: chr9-21178517;