rs34383331

Variant names:

• chr22-23895892-T-A
• rs34383331
• ENST00000406213.1:n.306A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate 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
• Publications: 16 publications found

Genes affected

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

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.028).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000406213.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	NR_038911.1		n.306A>T		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	ENST00000406213.1	TSL:1	n.306A>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000290199	ENST00000703580.1		n.605A>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000290199	ENST00000717616.1		n.213-4426A>T		intron	N/A

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

GnomAD2 exomes AF: 0.193 AC: 28746 AN: 148592 AF XY: 0.191

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 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

African (AFR) AF: 0.180 AC: 1544 AN: 8590

American (AMR) AF: 0.268 AC: 7263 AN: 27086

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 1506 AN: 10758

East Asian (EAS) AF: 0.210 AC: 1933 AN: 9206

South Asian (SAS) AF: 0.196 AC: 11688 AN: 59690

European-Finnish (FIN) AF: 0.214 AC: 5800 AN: 27110

Middle Eastern (MID) AF: 0.155 AC: 431 AN: 2778

European-Non Finnish (NFE) AF: 0.162 AC: 25797 AN: 158818

Other (OTH) AF: 0.175 AC: 2509 AN: 14334

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

African (AFR) AF: 0.175 AC: 7257 AN: 41502

American (AMR) AF: 0.223 AC: 3415 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 449 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5162

South Asian (SAS) AF: 0.197 AC: 949 AN: 4822

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10590

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11077 AN: 68002

Other (OTH) AF: 0.163 AC: 344 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs34383331;

hg19: chr22-24238079;

COSMIC: COSV107231842;