dbSNP rs7007634: MITA1:n.1374A>G (chr8-78807362-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007060969.1(MITA1):n.1374A>G 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 0.102 in 152,184 control chromosomes in the GnomAD database, including 866 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 0.10 ( 866 hom., cov: 32)

Consequence

MITA1
XR_007060969.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Publications

7 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MITA1	XR_007060969.1 link	n.1374A>G	non_coding_transcript_exon_variant	Exon 2 of 2
MITA1	XR_001745965.2 link	n.1224+1667A>G	intron_variant	Intron 1 of 2
MITA1	XR_001745967.2 link	n.1224+1667A>G	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+1667A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15604

AN:

152066

Hom.:

870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.0793

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0580

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.0923

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

GnomAD4 genome

AF:

0.102

AC:

15596

AN:

152184

Hom.:

866

Cov.:

AF XY:

0.101

AC XY:

7548

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.125

AC:

5194

AN:

41530

American (AMR)

AF:

0.0792

AC:

1211

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

407

AN:

3466

East Asian (EAS)

AF:

0.000771

AC:

AN:

5190

South Asian (SAS)

AF:

0.0568

AC:

274

AN:

4826

European-Finnish (FIN)

AF:

0.105

AC:

1110

AN:

10570

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6955

AN:

68002

Other (OTH)

AF:

0.0909

AC:

192

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

696

1392

2088

2784

3480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.101

Hom.:

429

Bravo

AF:

0.101

Asia WGS

AF:

0.0320

AC:

112

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.5

(source)

DANN

Benign

0.50

PhyloP100

-0.010

Splicing

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

Publications

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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