rs1007888

Variant names:

• chr22-23898914-C-T
• rs1007888
• ENST00000406213.1:n.17G>A

Variant summary

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

The ENST00000406213.1(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 ENST00000406213.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 56 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.604 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	NR_038911.1		n.17G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIF-AS1	ENST00000406213.1	TSL:1	n.17G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000290199	ENST00000703580.1		n.387-2804G>A		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.213-7448G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 8 AN: 16

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.246 AC: 10214 AN: 41450

American (AMR) AF: 0.509 AC: 7774 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2394 AN: 5154

South Asian (SAS) AF: 0.622 AC: 2999 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6477 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36974 AN: 67978

Other (OTH) AF: 0.464 AC: 980 AN: 2112

Alfa AF: 0.517 Hom.: 90597

Bravo AF: 0.443

Asia WGS AF: 0.526 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.68
PhyloP100		-2.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1007888;

hg19: chr22-24241101;

COSMIC: COSV53158774;