Genetic Variant ENST00000649603.2:n.517+44728C>T (chr8-78850423-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000649603.2(MITA1):n.517+44728C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,816 control chromosomes in the GnomAD database, including 15,168 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 0.44 ( 15168 hom., cov: 31)

Consequence

MITA1
ENST00000649603.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.241

Publications

4 publications found

Variant links:

Genes affected

MITA1 (HGNC:56733): (metabolism induced tumor activator 1)

MITA1 links:

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MITA1	XR_001745965.2 link	n.1224+44728C>T	intron_variant	Intron 1 of 2
MITA1	XR_001745967.2 link	n.1225-668C>T	intron_variant	Intron 1 of 3
MITA1	XR_001745970.2 link	n.1224+44728C>T	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MITA1	ENST00000649603.2 link	n.517+44728C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67139

AN:

151694

Hom.:

15159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.469

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.690

Gnomad SAS

AF:

0.365

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.381

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.443

AC:

67182

AN:

151816

Hom.:

15168

Cov.:

AF XY:

0.442

AC XY:

32794

AN XY:

74174

show subpopulations

African (AFR)

AF:

0.387

AC:

16020

AN:

41420

American (AMR)

AF:

0.469

AC:

7146

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1411

AN:

3468

East Asian (EAS)

AF:

0.690

AC:

3539

AN:

5132

South Asian (SAS)

AF:

0.365

AC:

1759

AN:

4818

European-Finnish (FIN)

AF:

0.453

AC:

4765

AN:

10520

Middle Eastern (MID)

AF:

0.381

AC:

112

AN:

294

European-Non Finnish (NFE)

AF:

0.456

AC:

30986

AN:

67918

Other (OTH)

AF:

0.454

AC:

957

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1905

3810

5715

7620

9525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.456

Hom.:

58708

Bravo

AF:

0.446

Asia WGS

AF:

0.523

AC:

1819

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.83

(source)

DANN

Benign

0.46

PhyloP100

-0.24

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over