Variant 16-56652558-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005947.3(MT1B):c.29-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,611,938 control chromosomes in the GnomAD database, including 167,173 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 0.41 ( 13396 hom., cov: 33)

Exomes 𝑓: 0.46 ( 153777 hom. )

Consequence

MT1B
NM_005947.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

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:

ENSG00000259923 (HGNC:):

ENSG00000259923 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MT1B	NM_005947.3 link	c.29-13C>T		intron_variant		ENST00000334346.3	NP_005938.1	P07438

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MT1B	ENST00000334346.3 link	c.29-13C>T	intron_variant	1	NM_005947.3	ENSP00000334998.2	P07438
MT1B	ENST00000562399.1 link	c.29-13C>T	intron_variant	3		ENSP00000456056.1	H3BR34
ENSG00000259923	ENST00000568608.1 link	n.179-13C>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62634

AN:

151978

Hom.:

13386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.567

Gnomad SAS

AF:

0.450

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.418

GnomAD3 exomes

AF:

0.459

AC:

115312

AN:

251350

Hom.:

27014

AF XY:

0.458

AC XY:

62255

AN XY:

135846

show subpopulations

Gnomad AFR exome

AF:

0.279

Gnomad AMR exome

AF:

0.531

Gnomad ASJ exome

AF:

0.404

Gnomad EAS exome

AF:

0.568

Gnomad SAS exome

AF:

0.457

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.449

Gnomad OTH exome

AF:

0.449

GnomAD4 exome

AF:

0.456

AC:

665648

AN:

1459842

Hom.:

153777

Cov.:

AF XY:

0.456

AC XY:

331083

AN XY:

726250

show subpopulations

Gnomad4 AFR exome

AF:

0.275

Gnomad4 AMR exome

AF:

0.530

Gnomad4 ASJ exome

AF:

0.400

Gnomad4 EAS exome

AF:

0.604

Gnomad4 SAS exome

AF:

0.453

Gnomad4 FIN exome

AF:

0.468

Gnomad4 NFE exome

AF:

0.455

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.412

AC:

62654

AN:

152096

Hom.:

13396

Cov.:

AF XY:

0.415

AC XY:

30865

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.486

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.452

Gnomad4 FIN

AF:

0.465

Gnomad4 NFE

AF:

0.452

Gnomad4 OTH

AF:

0.419

Alfa

AF:

0.370

Hom.:

2022

Bravo

AF:

0.410

Asia WGS

AF:

0.503

AC:

1752

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.8

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over