16-56683070-T-G

Position:

• chr16-56683070-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005952.4(MT1X):​c.29-95T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 1,456,520 control chromosomes in the GnomAD database, including 290,442 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 0.61 (29094 hom., cov: 33)
  • Exomes 𝑓: 0.63 (261348 hom.)
• Consequence: MT1X NM_005952.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

MT1X (HGNC:7405): (metallothionein 1X) Predicted to enable copper ion binding activity and zinc ion binding activity. Involved in cellular response to cadmium ion; cellular response to erythropoietin; and cellular response to zinc ion. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MT1X (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MT1X	NM_005952.4	c.29-95T>G		intron_variant		ENST00000394485.5	NP_005943.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT1X	ENST00000394485.5	c.29-95T>G		intron_variant		1	NM_005952.4	ENSP00000377995.4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93379 AN: 151982 Hom.: 29068 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.622

GnomAD4 exome AF: 0.630 AC: 821709 AN: 1304420 Hom.: 261348 Cov.: 18 AF XY: 0.628 AC XY: 410670 AN XY: 654426

Gnomad4 AFR exome AF: 0.548

Gnomad4 AMR exome AF: 0.696

Gnomad4 ASJ exome AF: 0.604

Gnomad4 EAS exome AF: 0.904

Gnomad4 SAS exome AF: 0.577

Gnomad4 FIN exome AF: 0.664

Gnomad4 NFE exome AF: 0.622

Gnomad4 OTH exome AF: 0.629

GnomAD4 genome AF: 0.614 AC: 93451 AN: 152100 Hom.: 29094 Cov.: 33 AF XY: 0.616 AC XY: 45825 AN XY: 74352

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.627

Alfa AF: 0.619 Hom.: 49096

Bravo AF: 0.613

Asia WGS AF: 0.752 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.52
DANN	Benign	0.47

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

Other links and lift over

dbSNP: rs2301234; hg19: chr16-56716982;