chr9-21420678-A-G

Position:

• chr9-21420678-A-G

Variant summary

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

The ENST00000431203.1(IFNWP2):​n.445A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 627,688 control chromosomes in the GnomAD database, including 13,730 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 0.23 (6702 hom., cov: 32)
  • Exomes 𝑓: 0.15 (7028 hom.)
• Consequence: IFNWP2 ENST00000431203.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

IFNWP2 (HGNC:5452): (interferon omega 1 pseudogene 2)

MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNWP2	ENST00000431203.1	n.445A>G		non_coding_transcript_exon_variant	1/1
MIR31HG	ENST00000698343.1	n.117T>C		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35668 AN: 151994 Hom.: 6676 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.147 AC: 70142 AN: 475574 Hom.: 7028 Cov.: 5 AF XY: 0.149 AC XY: 39354 AN XY: 263388

Gnomad4 AFR exome AF: 0.521

Gnomad4 AMR exome AF: 0.136

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.264

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.235 AC: 35746 AN: 152114 Hom.: 6702 Cov.: 32 AF XY: 0.233 AC XY: 17342 AN XY: 74372

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.202

Alfa AF: 0.130 Hom.: 2360

Bravo AF: 0.247

Asia WGS AF: 0.239 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1332179; hg19: chr9-21420677;