16-56652558-C-T

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

2

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]

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
MT1BNM_005947.3 linkc.29-13C>T intron_variant ENST00000334346.3 NP_005938.1 P07438

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MT1BENST00000334346.3 linkc.29-13C>T intron_variant 1 NM_005947.3 ENSP00000334998.2 P07438
MT1BENST00000562399.1 linkc.29-13C>T intron_variant 3 ENSP00000456056.1 H3BR34
ENSG00000259923ENST00000568608.1 linkn.179-13C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.412
AC:
62634
AN:
151978
Hom.:
13386
Cov.:
33
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.:
36
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.:
33
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.

Other links and lift over

dbSNP: rs12051311; hg19: chr16-56686470; COSMIC: COSV57618983; COSMIC: COSV57618983; API