9-21420678-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69
Variant links:
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]

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ACMG classification

Classification made for transcript

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
IFNWP2ENST00000431203.1 linkuse as main transcriptn.445A>G non_coding_transcript_exon_variant 1/1
MIR31HGENST00000698343.1 linkuse as main transcriptn.117T>C non_coding_transcript_exon_variant 2/5

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1332179; hg19: chr9-21420677; API