rs10433310

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_038911.1(MIF-AS1):​n.88-526C>T 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 0.323 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
NR_038911.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.856
Variant links:
Genes affected
MIF-AS1 (HGNC:27669): (MIF antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
MIF-AS1NR_038911.1 linkuse as main transcriptn.88-526C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIF-AS1ENST00000406213.1 linkuse as main transcriptn.88-526C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.323
AC:
49095
AN:
151830
Hom.:
7973
Cov.:
33
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.293
Gnomad4 AMR
AF:
0.396
Gnomad4 ASJ
AF:
0.293
Gnomad4 EAS
AF:
0.376
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.370
Gnomad4 NFE
AF:
0.318
Gnomad4 OTH
AF:
0.310
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10433310; hg19: chr22-24238823; API