dbSNP rs12448654: MT1G:c.28+51A>G (chr16-56667915-T-C) – 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.28+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,606,400 control chromosomes in the GnomAD database, including 14,989 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 0.11 ( 1030 hom., cov: 33)

Exomes 𝑓: 0.14 ( 13959 hom. )

Consequence

MT1G
NM_001301267.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.715

Publications

9 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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.28+51A>G		intron	N/A	NP_001288196.1	P13640-1
	MT1G	NM_005950.3		c.28+51A>G		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.28+51A>G	intron	N/A	ENSP00000369139.4	P13640-1
MT1G	ENST00000444837.6	TSL:1	c.28+51A>G	intron	N/A	ENSP00000391397.2	P13640-2
MT1G	ENST00000568675.1	TSL:1	n.56+51A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15973

AN:

152108

Hom.:

1030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0374

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0605

Gnomad EAS

AF:

0.0710

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.123

AC:

30974

AN:

251382

AF XY:

0.124

show subpopulations

Gnomad AFR exome

AF:

0.0337

Gnomad AMR exome

AF:

0.149

Gnomad ASJ exome

AF:

0.0590

Gnomad EAS exome

AF:

0.0674

Gnomad FIN exome

AF:

0.155

Gnomad NFE exome

AF:

0.140

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.135

AC:

197003

AN:

1454174

Hom.:

13959

Cov.:

AF XY:

0.135

AC XY:

97547

AN XY:

723890

show subpopulations

African (AFR)

AF:

0.0313

AC:

1042

AN:

33318

American (AMR)

AF:

0.145

AC:

6471

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.0569

AC:

1484

AN:

26064

East Asian (EAS)

AF:

0.0788

AC:

3121

AN:

39598

South Asian (SAS)

AF:

0.115

AC:

9868

AN:

86090

European-Finnish (FIN)

AF:

0.152

AC:

8084

AN:

53226

Middle Eastern (MID)

AF:

0.0724

AC:

416

AN:

5742

European-Non Finnish (NFE)

AF:

0.144

AC:

159492

AN:

1105364

Other (OTH)

AF:

0.117

AC:

7025

AN:

60102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

8599

17198

25797

34396

42995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5678

11356

17034

22712

28390

<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:

0.105

AC:

15985

AN:

152226

Hom.:

1030

Cov.:

AF XY:

0.104

AC XY:

7752

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0375

AC:

1557

AN:

41556

American (AMR)

AF:

0.117

AC:

1786

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0605

AC:

210

AN:

3470

East Asian (EAS)

AF:

0.0710

AC:

368

AN:

5182

South Asian (SAS)

AF:

0.108

AC:

520

AN:

4818

European-Finnish (FIN)

AF:

0.148

AC:

1573

AN:

10598

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.142

AC:

9638

AN:

67996

Other (OTH)

AF:

0.0993

AC:

210

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

732

1464

2195

2927

3659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.105

Hom.:

255

Bravo

AF:

0.0984

Asia WGS

AF:

0.0810

AC:

280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.4

(source)

DANN

Benign

0.53

PhyloP100

-0.71

PromoterAI

0.081

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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