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GeneBe

rs755622

Variant summary

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

The NR_038911.1(MIF-AS1):n.1697C>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 0.209 in 575,612 control chromosomes in the GnomAD database, including 14,325 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.25 ( 5807 hom., cov: 34)
Exomes 𝑓: 0.19 ( 8518 hom. )

Consequence

MIF-AS1
NR_038911.1 non_coding_transcript_exon

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.948
Variant links:
Genes affected

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIF-AS1NR_038911.1 linkuse as main transcriptn.1697C>G non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38654
AN:
152146
Hom.:
5790
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.410
Gnomad AMI
AF:
0.190
Gnomad AMR
AF:
0.261
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.201
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.232
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.174
Gnomad OTH
AF:
0.223
GnomAD4 exome
AF:
0.192
AC:
81356
AN:
423348
Hom.:
8518
Cov.:
0
AF XY:
0.194
AC XY:
43705
AN XY:
225798
show subpopulations
Gnomad4 AFR exome
AF:
0.402
Gnomad4 AMR exome
AF:
0.261
Gnomad4 ASJ exome
AF:
0.148
Gnomad4 EAS exome
AF:
0.212
Gnomad4 SAS exome
AF:
0.230
Gnomad4 FIN exome
AF:
0.230
Gnomad4 NFE exome
AF:
0.169
Gnomad4 OTH exome
AF:
0.205
GnomAD4 genome
AF:
0.254
AC:
38720
AN:
152264
Hom.:
5807
Cov.:
34
AF XY:
0.257
AC XY:
19136
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.410
Gnomad4 AMR
AF:
0.262
Gnomad4 ASJ
AF:
0.151
Gnomad4 EAS
AF:
0.201
Gnomad4 SAS
AF:
0.233
Gnomad4 FIN
AF:
0.232
Gnomad4 NFE
AF:
0.174
Gnomad4 OTH
AF:
0.219
Alfa
AF:
0.227
Hom.:
587
Bravo
AF:
0.259
Asia WGS
AF:
0.252
AC:
877
AN:
3478

ClinVar

Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Rheumatoid arthritis, systemic juvenile, susceptibility to Other:1
risk factor, no assertion criteria providedliterature onlyOMIMMay 01, 2003- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
2.8
Dann
Benign
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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: rs755622; hg19: chr22-24236392; API