22-23895892-T-A

Position:

• chr22-23895892-T-A

Variant summary

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

The ENST00000406213.1(MIF-AS1):​n.306A>T 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 0.182 in 470,526 control chromosomes in the GnomAD database, including 8,265 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 0.18 (2506 hom., cov: 32)
  • Exomes 𝑓: 0.18 (5759 hom.)
• Consequence: MIF-AS1 ENST00000406213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

MIF-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.306A>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.306A>T		non_coding_transcript_exon_variant	2/3	1
ENSG00000290199	ENST00000703580.1	n.605A>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26949 AN: 152038 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.166

GnomAD3 exomes AF: 0.193 AC: 28746 AN: 148592 Hom.: 3031 AF XY: 0.191 AC XY: 15254 AN XY: 80004

Gnomad AFR exome AF: 0.179

Gnomad AMR exome AF: 0.269

Gnomad ASJ exome AF: 0.138

Gnomad EAS exome AF: 0.212

Gnomad SAS exome AF: 0.195

Gnomad FIN exome AF: 0.221

Gnomad NFE exome AF: 0.158

Gnomad OTH exome AF: 0.185

GnomAD4 exome AF: 0.184 AC: 58471 AN: 318370 Hom.: 5759 Cov.: 0 AF XY: 0.184 AC XY: 33039 AN XY: 179932

Gnomad4 AFR exome AF: 0.180

Gnomad4 AMR exome AF: 0.268

Gnomad4 ASJ exome AF: 0.140

Gnomad4 EAS exome AF: 0.210

Gnomad4 SAS exome AF: 0.196

Gnomad4 FIN exome AF: 0.214

Gnomad4 NFE exome AF: 0.162

Gnomad4 OTH exome AF: 0.175

GnomAD4 genome AF: 0.177 AC: 26988 AN: 152156 Hom.: 2506 Cov.: 32 AF XY: 0.183 AC XY: 13584 AN XY: 74406

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.163

Alfa AF: 0.166 Hom.: 729

Bravo AF: 0.176

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34383331; hg19: chr22-24238079;