dbSNP rs708274: MT1E:c.*173G>T (chr16-56626994-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_001363555.2(MT1E):c.*173G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,613,590 control chromosomes in the GnomAD database, including 13,947 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 0.14 ( 1499 hom., cov: 33)

Exomes 𝑓: 0.13 ( 12448 hom. )

Consequence

MT1E
NM_001363555.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

Publications

26 publications found

Variant links:

Genes affected

MT1E (HGNC:7397): (metallothionein 1E) Predicted to enable zinc ion binding activity. Involved in cellular response to cadmium ion and cellular response to zinc ion. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MT1E 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1E	NM_001363555.2 link	c.*173G>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000330439.7	NP_001350484.1
MT1E	NM_175617.4 link	c.*23G>T		3_prime_UTR_variant	Exon 3 of 3		NP_783316.2	P04732-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MT1E	ENST00000330439.7 link	c.*173G>T	3_prime_UTR_variant	Exon 2 of 2	1	NM_001363555.2	ENSP00000328137.6	P04732-2
MT1E	ENST00000306061.10 link	c.*23G>T	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000307706.5	P04732-1
MT1E	ENST00000568293.1 link	c.*23G>T	3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000457516.1	H3BU80

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21147

AN:

152068

Hom.:

1495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.263

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0987

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.123

GnomAD2 exomes

AF:

0.141

AC:

35431

AN:

250716

AF XY:

0.140

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.248

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.121

GnomAD4 exome

AF:

0.128

AC:

186822

AN:

1461404

Hom.:

12448

Cov.:

AF XY:

0.128

AC XY:

93249

AN XY:

726998

show subpopulations

African (AFR)

AF:

0.159

AC:

5325

AN:

33456

American (AMR)

AF:

0.152

AC:

6776

AN:

44626

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

2836

AN:

26122

East Asian (EAS)

AF:

0.226

AC:

8981

AN:

39694

South Asian (SAS)

AF:

0.160

AC:

13790

AN:

86204

European-Finnish (FIN)

AF:

0.119

AC:

6363

AN:

53410

Middle Eastern (MID)

AF:

0.108

AC:

623

AN:

5764

European-Non Finnish (NFE)

AF:

0.120

AC:

133875

AN:

1111760

Other (OTH)

AF:

0.137

AC:

8253

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

9667

19334

29001

38668

48335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5012

10024

15036

20048

25060

<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:

0.139

AC:

21160

AN:

152186

Hom.:

1499

Cov.:

AF XY:

0.142

AC XY:

10530

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.158

AC:

6547

AN:

41498

American (AMR)

AF:

0.135

AC:

2062

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

368

AN:

3472

East Asian (EAS)

AF:

0.245

AC:

1269

AN:

5178

South Asian (SAS)

AF:

0.174

AC:

838

AN:

4828

European-Finnish (FIN)

AF:

0.127

AC:

1345

AN:

10598

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.120

AC:

8193

AN:

68004

Other (OTH)

AF:

0.128

AC:

270

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

963

1925

2888

3850

4813

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.119

Hom.:

870

Bravo

AF:

0.140

Asia WGS

AF:

0.198

AC:

687

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.2

(source)

DANN

Benign

0.76

PhyloP100

-1.2

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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