rs755622

Positions:

• chr22-23894205-G-C

Variant summary

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

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
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.948

Genes affected

MIF-AS1 (HGNC:):

ACMG classification

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	Protein	UniProt
MIF-AS1	NR_038911.1	n.1697C>G		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38654 AN: 152146 Hom.: 5790 Cov.: 34

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

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

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

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	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

Other links and lift over

dbSNP: rs755622; hg19: chr22-24236392;