rs2000466

Positions:

• chr22-23895675-T-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.370-143A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 403,330 control chromosomes in the GnomAD database, including 8,639 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 0.21 (3487 hom., cov: 32)
  • Exomes 𝑓: 0.19 (5152 hom.)
• Consequence: MIF-AS1 NR_038911.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949

Genes affected

MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.370-143A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.370-143A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31447 AN: 151964 Hom.: 3476 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.195 AC: 48978 AN: 251248 Hom.: 5152 Cov.: 0 AF XY: 0.197 AC XY: 27715 AN XY: 140656

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.211

Gnomad4 SAS exome AF: 0.224

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.185

GnomAD4 genome AF: 0.207 AC: 31491 AN: 152082 Hom.: 3487 Cov.: 32 AF XY: 0.211 AC XY: 15710 AN XY: 74326

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.184

Alfa AF: 0.188 Hom.: 1290

Bravo AF: 0.208

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2000466; hg19: chr22-24237862;