dbSNP rs2298846: MT1G:c.29-23T>C (chr16-56667403-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 NM_001301267.2(MT1G):c.29-23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 1,608,418 control chromosomes in the GnomAD database, including 2,068 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 0.051 ( 239 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1829 hom. )

Consequence

MT1G
NM_001301267.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

4 publications found

Variant links:

Genes affected

MT1G (HGNC:7399): (metallothionein 1G) Enables zinc ion binding activity. Involved in cellular response to metal ion; cellular response to vascular endothelial growth factor stimulus; and negative regulation of growth. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MT1G 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001301267.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT1G	NM_001301267.2	MANE Select	c.29-23T>C		intron	N/A	NP_001288196.1	P13640-1
	MT1G	NM_005950.3		c.29-26T>C		intron	N/A	NP_005941.1	P13640-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MT1G	ENST00000379811.4	TSL:1 MANE Select	c.29-23T>C	intron	N/A	ENSP00000369139.4	P13640-1
MT1G	ENST00000444837.6	TSL:1	c.29-26T>C	intron	N/A	ENSP00000391397.2	P13640-2
MT1G	ENST00000568675.1	TSL:1	n.57-26T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0508

AC:

7598

AN:

149436

Hom.:

239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.0880

Gnomad ASJ

AF:

0.0349

Gnomad EAS

AF:

0.0577

Gnomad SAS

AF:

0.0782

Gnomad FIN

AF:

0.0555

Gnomad MID

AF:

0.0288

Gnomad NFE

AF:

0.0366

Gnomad OTH

AF:

0.0426

GnomAD2 exomes

AF:

0.0571

AC:

14318

AN:

250894

AF XY:

0.0561

show subpopulations

Gnomad AFR exome

AF:

0.0552

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.0356

Gnomad EAS exome

AF:

0.0534

Gnomad FIN exome

AF:

0.0553

Gnomad NFE exome

AF:

0.0342

Gnomad OTH exome

AF:

0.0471

GnomAD4 exome

AF:

0.0446

AC:

64996

AN:

1458872

Hom.:

1829

Cov.:

AF XY:

0.0453

AC XY:

32912

AN XY:

725998

show subpopulations

African (AFR)

AF:

0.0581

AC:

1819

AN:

31322

American (AMR)

AF:

0.118

AC:

5248

AN:

44538

Ashkenazi Jewish (ASJ)

AF:

0.0338

AC:

882

AN:

26122

East Asian (EAS)

AF:

0.0710

AC:

2819

AN:

39682

South Asian (SAS)

AF:

0.0839

AC:

7230

AN:

86218

European-Finnish (FIN)

AF:

0.0556

AC:

2967

AN:

53366

Middle Eastern (MID)

AF:

0.0369

AC:

212

AN:

5744

European-Non Finnish (NFE)

AF:

0.0368

AC:

40916

AN:

1111782

Other (OTH)

AF:

0.0483

AC:

2903

AN:

60098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

3479

6958

10437

13916

17395

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1702

3404

5106

6808

8510

<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:

0.0509

AC:

7609

AN:

149546

Hom.:

239

Cov.:

AF XY:

0.0525

AC XY:

3835

AN XY:

73116

show subpopulations

African (AFR)

AF:

0.0586

AC:

2285

AN:

38968

American (AMR)

AF:

0.0877

AC:

1332

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.0349

AC:

121

AN:

3472

East Asian (EAS)

AF:

0.0578

AC:

299

AN:

5174

South Asian (SAS)

AF:

0.0789

AC:

381

AN:

4830

European-Finnish (FIN)

AF:

0.0555

AC:

589

AN:

10622

Middle Eastern (MID)

AF:

0.0241

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0365

AC:

2485

AN:

67994

Other (OTH)

AF:

0.0421

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

369

738

1108

1477

1846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0455

Hom.:

Bravo

AF:

0.0625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.8

(source)

DANN

Benign

0.29

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over