rs1332179

Variant names:

• chr9-21420678-A-G
• rs1332179
• ENST00000431203.1:n.445A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-21420678-A-G
• chr9-21420678-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IFNWP2		n.21420678A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNWP2	ENST00000431203.1	n.445A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR31HG	ENST00000669680.1	n.2283T>C		non_coding_transcript_exon_variant	Exon 1 of 3
MIR31HG	ENST00000698343.1	n.117T>C		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.521 AC: 6912 AN: 13274

American (AMR) AF: 0.136 AC: 4544 AN: 33370

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 2050 AN: 13856

East Asian (EAS) AF: 0.264 AC: 6984 AN: 26504

South Asian (SAS) AF: 0.222 AC: 12397 AN: 55796

European-Finnish (FIN) AF: 0.113 AC: 3621 AN: 31980

Middle Eastern (MID) AF: 0.216 AC: 710 AN: 3280

European-Non Finnish (NFE) AF: 0.107 AC: 29028 AN: 272510

Other (OTH) AF: 0.156 AC: 3896 AN: 25004

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

African (AFR) AF: 0.518 AC: 21458 AN: 41460

American (AMR) AF: 0.162 AC: 2471 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 475 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1278 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1229 AN: 10606

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7104 AN: 67982

Other (OTH) AF: 0.202 AC: 428 AN: 2114

Alfa AF: 0.142 Hom.: 3888

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1332179; hg19: chr9-21420677;