rs9282783

chr22-23894172-C-G

Variant summary

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

The NR_038911.1(MIF-AS1):n.1730G>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 0.0122 in 539,296 control chromosomes in the GnomAD database, including 229 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 0.027 (167 hom., cov: 33)
  • Exomes 𝑓: 0.0062 (62 hom.)
• Consequence: MIF-AS1 NR_038911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

MIF-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIF-AS1	NR_038911.1	n.1730G>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4139 AN: 152290 Hom.: 162 Cov.: 33

Gnomad AFR AF: 0.0898

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000411

Gnomad OTH AF: 0.0205

GnomAD4 exome AF: 0.00618 AC: 2392 AN: 386888 Hom.: 62 Cov.: 0 AF XY: 0.00747 AC XY: 1531 AN XY: 205058

Gnomad4 AFR exome AF: 0.0848

Gnomad4 AMR exome AF: 0.0107

Gnomad4 ASJ exome AF: 0.00131

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0305

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000358

Gnomad4 OTH exome AF: 0.0108

GnomAD4 genome AF: 0.0273 AC: 4161 AN: 152408 Hom.: 167 Cov.: 33 AF XY: 0.0268 AC XY: 1999 AN XY: 74532

Gnomad4 AFR AF: 0.0900

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000411

Gnomad4 OTH AF: 0.0203

Alfa AF: 0.0162 Hom.: 12

Bravo AF: 0.0310

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.78
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs9282783; hg19: chr22-24236359;