rs1007888

Positions:

• chr22-23898914-C-T

Variant summary

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

The NR_038911.1(MIF-AS1):​n.17G>A 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 0.461 in 152,062 control chromosomes in the GnomAD database, including 17,657 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 0.46 (17653 hom., cov: 32)
  • Exomes 𝑓: 0.58 (4 hom.)
• Consequence: MIF-AS1 NR_038911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94

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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIF-AS1	NR_038911.1	n.17G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIF-AS1	ENST00000406213.1	n.17G>A		non_coding_transcript_exon_variant	1/3	1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70102 AN: 151920 Hom.: 17640 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.463

GnomAD4 exome AF: 0.583 AC: 14 AN: 24 Hom.: 4 Cov.: 0 AF XY: 0.500 AC XY: 10 AN XY: 20

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.461 AC: 70126 AN: 152038 Hom.: 17653 Cov.: 32 AF XY: 0.470 AC XY: 34932 AN XY: 74322

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.464

Alfa AF: 0.529 Hom.: 43411

Bravo AF: 0.443

Asia WGS AF: 0.526 AC: 1831 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	0.21
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007888; hg19: chr22-24241101; COSMIC: COSV53158774;