dbSNP rs8052334: MT1B:c.95-68T>C (chr16-56652906-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_005947.3(MT1B):c.95-68T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 1,542,142 control chromosomes in the GnomAD database, including 197,693 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 0.46 ( 16687 hom., cov: 33)

Exomes 𝑓: 0.51 ( 181006 hom. )

Consequence

MT1B
NM_005947.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

17 publications found

Variant links:

Genes affected

MT1B (HGNC:7394): (metallothionein 1B) The protein encoded by this gene binds heavy metals and protects against toxicity from heavy metal ions. This gene is found in a cluster of similar genes on chromosome 16. [provided by RefSeq, Jul 2016]

MT1B 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MT1B	NM_005947.3 link	c.95-68T>C		intron_variant	Intron 2 of 2	ENST00000334346.3	NP_005938.1	P07438

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT1B	ENST00000334346.3 link	c.95-68T>C		intron_variant	Intron 2 of 2	1	NM_005947.3	ENSP00000334998.2		P07438
MT1B	ENST00000562399.1 link	c.93-68T>C		intron_variant	Intron 2 of 2	3		ENSP00000456056.1		H3BR34

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

70083

AN:

151936

Hom.:

16679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.794

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.515

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.474

GnomAD4 exome

AF:

0.507

AC:

704499

AN:

1390088

Hom.:

181006

AF XY:

0.509

AC XY:

353792

AN XY:

695752

show subpopulations

African (AFR)

AF:

0.340

AC:

10860

AN:

31930

American (AMR)

AF:

0.404

AC:

18014

AN:

44590

Ashkenazi Jewish (ASJ)

AF:

0.505

AC:

12946

AN:

25618

East Asian (EAS)

AF:

0.308

AC:

12119

AN:

39300

South Asian (SAS)

AF:

0.518

AC:

43803

AN:

84574

European-Finnish (FIN)

AF:

0.509

AC:

27020

AN:

53100

Middle Eastern (MID)

AF:

0.513

AC:

2175

AN:

4236

European-Non Finnish (NFE)

AF:

0.523

AC:

548959

AN:

1048934

Other (OTH)

AF:

0.495

AC:

28603

AN:

57806

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

18008

36016

54023

72031

90039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15188

30376

45564

60752

75940

<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:

0.461

AC:

70122

AN:

152054

Hom.:

16687

Cov.:

AF XY:

0.462

AC XY:

34333

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.347

AC:

14387

AN:

41460

American (AMR)

AF:

0.446

AC:

6815

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

1741

AN:

3468

East Asian (EAS)

AF:

0.323

AC:

1669

AN:

5174

South Asian (SAS)

AF:

0.514

AC:

2478

AN:

4822

European-Finnish (FIN)

AF:

0.515

AC:

5450

AN:

10574

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.526

AC:

35732

AN:

67956

Other (OTH)

AF:

0.473

AC:

999

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1938

3876

5815

7753

9691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<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:

0.469

Hom.:

2545

Bravo

AF:

0.448

Asia WGS

AF:

0.411

AC:

1427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.5

(source)

DANN

Benign

0.59

PhyloP100

-1.3

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