16-56644953-T-G

Variant names:

• chr16-56644953-T-G
• rs8044719
• ENST00000849205.1:n.158+777T>G

Variant summary

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

The ENST00000849205.1(ENSG00000291095):​n.158+777T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,146 control chromosomes in the GnomAD database, including 48,465 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 0.79 (48465 hom., cov: 32)
• Consequence: ENSG00000291095 ENST00000849205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 12 publications found

Genes affected

ENSG00000291095 (HGNC:):

MT1DP (HGNC:7396): (metallothionein 1D, pseudogene) Predicted to enable metal ion binding activity. Predicted to be involved in cellular response to metal ion; cellular zinc ion homeostasis; and detoxification of copper ion. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT1DP	NR_003658.2		n.*12T>G		downstream_gene	N/A
	MT1DP	NR_027781.1		n.*12T>G		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291095	ENST00000849205.1		n.158+777T>G		intron	N/A
	ENSG00000291095	ENST00000463480.8	TSL:1	n.*11T>G		downstream_gene	N/A
	MT1DP	ENST00000486551.1	TSL:6	n.*188T>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120441 AN: 152028 Hom.: 48448 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.792 AC: 120499 AN: 152146 Hom.: 48465 Cov.: 32 AF XY: 0.797 AC XY: 59324 AN XY: 74406

African (AFR) AF: 0.632 AC: 26206 AN: 41466

American (AMR) AF: 0.844 AC: 12909 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3086 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4554 AN: 5178

South Asian (SAS) AF: 0.858 AC: 4136 AN: 4820

European-Finnish (FIN) AF: 0.849 AC: 9006 AN: 10606

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57871 AN: 67998

Other (OTH) AF: 0.811 AC: 1709 AN: 2106

Alfa AF: 0.827 Hom.: 18718

Bravo AF: 0.785

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.059
DANN	Benign	0.57
PhyloP100		-3.0

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: rs8044719; hg19: chr16-56678865;