ENST00000406213.1:n.88-946A>C

Variant names:

• chr22-23897056-T-G
• rs1007889
• ENST00000406213.1:n.88-946A>C

Variant summary

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

The ENST00000406213.1(MIF-AS1):​n.88-946A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,526 control chromosomes in the GnomAD database, including 8,547 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 0.33 (8547 hom., cov: 31)
• Consequence: MIF-AS1 ENST00000406213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

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

ENSG00000290199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.88-946A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.88-946A>C		intron_variant	Intron 1 of 2	1
ENSG00000290199	ENST00000703580.1	n.387-946A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50634 AN: 151406 Hom.: 8533 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.334 AC: 50671 AN: 151526 Hom.: 8547 Cov.: 31 AF XY: 0.337 AC XY: 24931 AN XY: 73988

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.322

Alfa AF: 0.262 Hom.: 1176

Bravo AF: 0.333

Asia WGS AF: 0.345 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007889; hg19: chr22-24239243;