Genetic Variant MT1G:n.624C>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 ENST00000568675.1(MT1G):n.624C>A 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 0.0757 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
ENST00000568675.1 non_coding_transcript_exon

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:

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1G	NM_001301267.2 link	c.*69C>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000379811.4	NP_001288196.1	P13640-1
MT1G	NM_005950.3 link	c.*69C>A		3_prime_UTR_variant	Exon 3 of 3		NP_005941.1	P13640-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MT1G	ENST00000568675.1 link	n.624C>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
MT1G	ENST00000379811.4 link	c.*69C>A	3_prime_UTR_variant	Exon 3 of 3	1	NM_001301267.2	ENSP00000369139.4	P13640-1
MT1G	ENST00000444837.6 link	c.*69C>A	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000391397.2	P13640-2
MT1G	ENST00000569500.5 link	c.*69C>A	3_prime_UTR_variant	Exon 2 of 2	3		ENSP00000456675.1	H3BSF1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over