Variant rs8052334 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.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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MT1B	NM_005947.3 linkuse as main transcript	c.95-68T>C		intron_variant		ENST00000334346.3	NP_005938.1	P07438

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT1B	ENST00000334346.3 linkuse as main transcript	c.95-68T>C		intron_variant		1	NM_005947.3	ENSP00000334998.2		P07438
MT1B	ENST00000562399.1 linkuse as main transcript	c.93-68T>C		intron_variant		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

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.404

Gnomad4 ASJ exome

AF:

0.505

Gnomad4 EAS exome

AF:

0.308

Gnomad4 SAS exome

AF:

0.518

Gnomad4 FIN exome

AF:

0.509

Gnomad4 NFE exome

AF:

0.523

Gnomad4 OTH exome

AF:

0.495

GnomAD4 genome

AF:

0.461

AC:

70122

AN:

152054

Hom.:

16687

Cov.:

AF XY:

0.462

AC XY:

34333

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.347

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.502

Gnomad4 EAS

AF:

0.323

Gnomad4 SAS

AF:

0.514

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.526

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.473

Hom.:

2492

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

DANN

Benign

0.59

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

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