GeneBe

8-78840775-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000649603.2(MITA1):​n.517+35080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,134 control chromosomes in the GnomAD database, including 41,288 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 0.72 ( 41288 hom., cov: 33)

Consequence

MITA1
ENST00000649603.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.803

Publications

7 publications found
Variant links:
Genes affected
MITA1 (HGNC:56733): (metabolism induced tumor activator 1)
LINC02605 (HGNC:53974): (long intergenic non-protein coding RNA 2605)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MITA1XR_001745965.2 linkn.1224+35080C>T intron_variant Intron 1 of 2
MITA1XR_001745967.2 linkn.1225-10316C>T intron_variant Intron 1 of 3
MITA1XR_001745970.2 linkn.1224+35080C>T intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MITA1ENST00000649603.2 linkn.517+35080C>T intron_variant Intron 1 of 5
LINC02605ENST00000565297.2 linkn.*250C>T downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.723
AC:
109887
AN:
152016
Hom.:
41231
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.934
Gnomad AMI
AF:
0.529
Gnomad AMR
AF:
0.707
Gnomad ASJ
AF:
0.624
Gnomad EAS
AF:
0.883
Gnomad SAS
AF:
0.602
Gnomad FIN
AF:
0.617
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.619
Gnomad OTH
AF:
0.717
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.723
AC:
110001
AN:
152134
Hom.:
41288
Cov.:
33
AF XY:
0.721
AC XY:
53592
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.934
AC:
38808
AN:
41538
American (AMR)
AF:
0.707
AC:
10801
AN:
15272
Ashkenazi Jewish (ASJ)
AF:
0.624
AC:
2166
AN:
3470
East Asian (EAS)
AF:
0.883
AC:
4559
AN:
5164
South Asian (SAS)
AF:
0.601
AC:
2898
AN:
4820
European-Finnish (FIN)
AF:
0.617
AC:
6517
AN:
10564
Middle Eastern (MID)
AF:
0.639
AC:
188
AN:
294
European-Non Finnish (NFE)
AF:
0.619
AC:
42068
AN:
67988
Other (OTH)
AF:
0.717
AC:
1514
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1464
2928
4393
5857
7321
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
814
1628
2442
3256
4070
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.655
Hom.:
45552
Bravo
AF:
0.741
Asia WGS
AF:
0.759
AC:
2641
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.8
DANN
Benign
0.76
PhyloP100
-0.80

Splicing

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

Publications

Other links and lift over

dbSNP: rs4739140; hg19: chr8-79753010; API