rs755622

Variant summary

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

The NR_038911(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 0.254 in 152146 control chromosomes in the gnomAD Genomes database, including 5790 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 ( 5790 hom., cov: 34)

Consequence

MIF-AS1
NR_038911 non_coding_transcript_exon

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.948

Links

MIF-AS1 (HGNC:):

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

GnomAd 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-AS1	NR_038911.1 linkuse as main transcript	n.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.:

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

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

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 provided

literature only

OMIM

May 01, 2003

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

Cadd

Benign

5.9

Dann

Benign

0.45

Splicing

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

Publications

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over