NM_005947.3:c.29-241C>T

Variant names:

• chr16-56652330-C-T
• rs2070839
• NM_005947.3:c.29-241C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 publications found

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]

ENSG00000259923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005947.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT1B	NM_005947.3	MANE Select	c.29-241C>T		intron	N/A	NP_005938.1	P07438

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT1B	ENST00000334346.3	TSL:1 MANE Select	c.29-241C>T		intron	N/A	ENSP00000334998.2	P07438
	MT1B	ENST00000562399.1	TSL:3	c.29-241C>T		intron	N/A	ENSP00000456056.1	H3BR34
	ENSG00000259923	ENST00000568608.1	TSL:5	n.179-241C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51590 AN: 151936 Hom.: 9102 Cov.: 33

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.: 33 AF XY: 0.343 AC XY: 25470 AN XY: 74316

African (AFR) AF: 0.250 AC: 10357 AN: 41486

American (AMR) AF: 0.410 AC: 6269 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2039 AN: 5160

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4635 AN: 10584

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24987 AN: 67944

Other (OTH) AF: 0.338 AC: 709 AN: 2100

Alfa AF: 0.353 Hom.: 14497

Bravo AF: 0.337

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.45
PhyloP100		-1.1
PromoterAI		-0.029	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2070839; hg19: chr16-56686242; COSMIC: COSV57618995; COSMIC: COSV57618995;