rs2000466

Variant names:

• chr22-23895675-T-G
• rs2000466
• ENST00000406213.1:n.370-143A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000406213.1(MIF-AS1):​n.370-143A>C variant causes a intron 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 ENST00000406213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949
• Publications: 22 publications found

Genes affected

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

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.370-143A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.370-143A>C		intron_variant	Intron 2 of 2	1
ENSG00000290199	ENST00000703580.1	n.822A>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000290199	ENST00000717616.1	n.213-4209A>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.260 AC: 1754 AN: 6758

American (AMR) AF: 0.271 AC: 5254 AN: 19410

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 908 AN: 6550

East Asian (EAS) AF: 0.211 AC: 1859 AN: 8826

South Asian (SAS) AF: 0.224 AC: 11201 AN: 49966

European-Finnish (FIN) AF: 0.217 AC: 3496 AN: 16100

Middle Eastern (MID) AF: 0.165 AC: 158 AN: 960

European-Non Finnish (NFE) AF: 0.169 AC: 22198 AN: 131082

Other (OTH) AF: 0.185 AC: 2150 AN: 11596

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

African (AFR) AF: 0.258 AC: 10695 AN: 41472

American (AMR) AF: 0.238 AC: 3635 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5170

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4824

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10592

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11596 AN: 67960

Other (OTH) AF: 0.184 AC: 387 AN: 2108

Alfa AF: 0.186 Hom.: 1433

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
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs2000466; hg19: chr22-24237862; COSMIC: COSV107231841;