rs10433310

Variant names:

• chr22-23896636-G-A
• rs10433310
• ENST00000406213.1:n.88-526C>T

Variant summary

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

The ENST00000406213.1(MIF-AS1):​n.88-526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,948 control chromosomes in the GnomAD database, including 7,985 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 0.32 (7985 hom., cov: 33)
• Consequence: MIF-AS1 ENST00000406213.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.88-526C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.88-526C>T		intron_variant	Intron 1 of 2	1
ENSG00000290199	ENST00000703580.1	n.387-526C>T		intron_variant	Intron 3 of 3
ENSG00000290199	ENST00000717616.1	n.213-5170C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49095 AN: 151830 Hom.: 7973 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.323 AC: 49132 AN: 151948 Hom.: 7985 Cov.: 33 AF XY: 0.326 AC XY: 24207 AN XY: 74258

African (AFR) AF: 0.293 AC: 12158 AN: 41454

American (AMR) AF: 0.396 AC: 6056 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1018 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1935 AN: 5152

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4820

European-Finnish (FIN) AF: 0.370 AC: 3902 AN: 10548

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21582 AN: 67918

Other (OTH) AF: 0.310 AC: 655 AN: 2114

Alfa AF: 0.321 Hom.: 972

Bravo AF: 0.324

Asia WGS AF: 0.330 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.61
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10433310; hg19: chr22-24238823;