dbSNP rs12315: MT1G:c.*69C>A (chr16-56666810-G-T) – 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.*69C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0757 in 1,584,032 control chromosomes in the GnomAD database, including 6,045 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 0.081 ( 704 hom., cov: 33)

Exomes 𝑓: 0.075 ( 5341 hom. )

Consequence

MT1G
NM_001301267.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.56

Publications

10 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:

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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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 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.*69C>A		3_prime_UTR	Exon 3 of 3	NP_001288196.1	P13640-1
	MT1G	NM_005950.3		c.*69C>A		3_prime_UTR	Exon 3 of 3	NP_005941.1	P13640-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MT1G	ENST00000379811.4	TSL:1 MANE Select	c.*69C>A	3_prime_UTR	Exon 3 of 3	ENSP00000369139.4	P13640-1
MT1G	ENST00000444837.6	TSL:1	c.*69C>A	3_prime_UTR	Exon 3 of 3	ENSP00000391397.2	P13640-2
MT1G	ENST00000568675.1	TSL:1	n.624C>A	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0805

AC:

12248

AN:

152152

Hom.:

701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0579

Gnomad AMI

AF:

0.0451

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.0879

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.0334

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0633

Gnomad OTH

AF:

0.0864

GnomAD4 exome

AF:

0.0752

AC:

107656

AN:

1431762

Hom.:

5341

Cov.:

AF XY:

0.0758

AC XY:

53806

AN XY:

710272

show subpopulations

African (AFR)

AF:

0.0557

AC:

1793

AN:

32210

American (AMR)

AF:

0.222

AC:

8557

AN:

38544

Ashkenazi Jewish (ASJ)

AF:

0.0836

AC:

2040

AN:

24392

East Asian (EAS)

AF:

0.215

AC:

8470

AN:

39404

South Asian (SAS)

AF:

0.126

AC:

10324

AN:

81956

European-Finnish (FIN)

AF:

0.0345

AC:

1818

AN:

52698

Middle Eastern (MID)

AF:

0.0880

AC:

495

AN:

5628

European-Non Finnish (NFE)

AF:

0.0632

AC:

69346

AN:

1097898

Other (OTH)

AF:

0.0815

AC:

4813

AN:

59032

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

5065

10131

15196

20262

25327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2870

5740

8610

11480

14350

<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:

0.0805

AC:

12265

AN:

152270

Hom.:

704

Cov.:

AF XY:

0.0836

AC XY:

6223

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0579

AC:

2408

AN:

41554

American (AMR)

AF:

0.182

AC:

2786

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0879

AC:

305

AN:

3470

East Asian (EAS)

AF:

0.240

AC:

1244

AN:

5182

South Asian (SAS)

AF:

0.126

AC:

609

AN:

4830

European-Finnish (FIN)

AF:

0.0334

AC:

355

AN:

10616

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0633

AC:

4305

AN:

68002

Other (OTH)

AF:

0.0888

AC:

188

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

573

1146

1718

2291

2864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0716

Hom.:

369

Bravo

AF:

0.0900

Asia WGS

AF:

0.164

AC:

567

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.16

(source)

DANN

Benign

0.47

PhyloP100

-2.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

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