chr22-23897708-T-C

Variant names:

• chr22-23897708-T-C
• rs17004044
• ENST00000406213.1:n.87+1136A>G

Variant summary

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

The ENST00000406213.1(MIF-AS1):​n.87+1136A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 148,718 control chromosomes in the GnomAD database, including 6,649 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 0.28 (6649 hom., cov: 26)
• Consequence: MIF-AS1 ENST00000406213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	NR_038911.1		n.87+1136A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	ENST00000406213.1	TSL:1	n.87+1136A>G		intron	N/A
	ENSG00000290199	ENST00000703580.1		n.387-1598A>G		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.213-6242A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42013 AN: 148604 Hom.: 6637 Cov.: 26

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.289

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.283 AC: 42056 AN: 148718 Hom.: 6649 Cov.: 26 AF XY: 0.278 AC XY: 20112 AN XY: 72450

African (AFR) AF: 0.420 AC: 16703 AN: 39756

American (AMR) AF: 0.268 AC: 3993 AN: 14916

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1067 AN: 3448

East Asian (EAS) AF: 0.177 AC: 895 AN: 5056

South Asian (SAS) AF: 0.186 AC: 879 AN: 4720

European-Finnish (FIN) AF: 0.189 AC: 1902 AN: 10088

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15656 AN: 67482

Other (OTH) AF: 0.285 AC: 589 AN: 2064

Alfa AF: 0.230 Hom.: 1384

Bravo AF: 0.302

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.29
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs17004044; hg19: chr22-24239895;