rs17004044

Positions:

• chr22-23897708-T-C
• chr22-23897708-T-G

Variant summary

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

The NR_038911.1(MIF-AS1):​n.87+1136A>G variant causes a intron, non coding transcript 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 NR_038911.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIF-AS1	NR_038911.1	n.87+1136A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.87+1136A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.285

Alfa AF: 0.187 Hom.: 511

Bravo AF: 0.302

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17004044; hg19: chr22-24239895;