Genetic Variant MT1JP:n.*22C>A (chr16-56637108-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000563395.5(MT1JP):n.*22C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 568,024 control chromosomes in the GnomAD database, including 36,226 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 0.34 ( 9038 hom., cov: 33)

Exomes 𝑓: 0.36 ( 27188 hom. )

Consequence

MT1JP
ENST00000563395.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.90

Publications

9 publications found

Variant links:

Genes affected

MT1JP (HGNC:):

MT1JP links:

MT1JP (HGNC:7402): (metallothionein 1J, pseudogene)

MT1JP 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1JP	NR_036677.1 link	n.*22C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MT1JP	ENST00000563395.5 link	n.*22C>A	downstream_gene_variant	1
MT1JP	ENST00000444023.4 link	n.*165C>A	downstream_gene_variant	6
MT1JP	ENST00000564564.1 link	n.*112C>A	downstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.343

AC:

52020

AN:

151844

Hom.:

9028

Cov.:

show subpopulations

Gnomad AFR

AF:

0.326

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.352

GnomAD4 exome

AF:

0.355

AC:

147734

AN:

416062

Hom.:

27188

Cov.:

AF XY:

0.361

AC XY:

78565

AN XY:

217912

show subpopulations

African (AFR)

AF:

0.323

AC:

3458

AN:

10704

American (AMR)

AF:

0.332

AC:

5296

AN:

15934

Ashkenazi Jewish (ASJ)

AF:

0.381

AC:

4114

AN:

10798

East Asian (EAS)

AF:

0.373

AC:

8355

AN:

22406

South Asian (SAS)

AF:

0.461

AC:

19963

AN:

43274

European-Finnish (FIN)

AF:

0.303

AC:

6210

AN:

20478

Middle Eastern (MID)

AF:

0.315

AC:

1002

AN:

3180

European-Non Finnish (NFE)

AF:

0.342

AC:

91528

AN:

267344

Other (OTH)

AF:

0.356

AC:

7808

AN:

21944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

4586

9172

13759

18345

22931

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1212

2424

3636

4848

6060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.343

AC:

52054

AN:

151962

Hom.:

9038

Cov.:

AF XY:

0.342

AC XY:

25384

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.326

AC:

13505

AN:

41462

American (AMR)

AF:

0.327

AC:

4991

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1326

AN:

3472

East Asian (EAS)

AF:

0.417

AC:

2151

AN:

5160

South Asian (SAS)

AF:

0.467

AC:

2247

AN:

4812

European-Finnish (FIN)

AF:

0.294

AC:

3086

AN:

10506

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23505

AN:

67966

Other (OTH)

AF:

0.355

AC:

747

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1810

3620

5431

7241

9051

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.313

Hom.:

3265

Bravo

AF:

0.339

Asia WGS

AF:

0.409

AC:

1423

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.090

(source)

DANN

Benign

0.44

PhyloP100

-3.9

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over