Variant 16-56652330-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.29-241C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,054 control chromosomes in the GnomAD database, including 9,114 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 0.34 ( 9114 hom., cov: 33)

Consequence

MT1B
NM_005947.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MT1B	NM_005947.3 linkuse as main transcript	c.29-241C>T		intron_variant		ENST00000334346.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT1B	ENST00000334346.3 linkuse as main transcript	c.29-241C>T		intron_variant		1	NM_005947.3	P1
MT1B	ENST00000562399.1 linkuse as main transcript	c.29-241C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.340

AC:

51590

AN:

151936

Hom.:

9102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.155

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.337

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.339

AC:

51612

AN:

152054

Hom.:

9114

Cov.:

AF XY:

0.343

AC XY:

25470

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.410

Gnomad4 ASJ

AF:

0.282

Gnomad4 EAS

AF:

0.395

Gnomad4 SAS

AF:

0.287

Gnomad4 FIN

AF:

0.438

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.338

Alfa

AF:

0.357

Hom.:

10252

Bravo

AF:

0.337

Asia WGS

AF:

0.363

AC:

1265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.77

DANN

Benign

0.45

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