rs1332179

Positions:

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

Variant summary

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

The ENST00000669680.1(MIR31HG):​n.2283T>C 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: MIR31HG ENST00000669680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

IFNWP2 (HGNC:):

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
IFNWP2		n.21420678A>G		intragenic_variant

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	6
MIR31HG	ENST00000669680.1	n.2283T>C		non_coding_transcript_exon_variant	1/3
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;