16-56644953-T-G

Position:

• chr16-56644953-T-G

Variant summary

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

The 16-56644953-T-G variant causes a downstream gene 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: MT1DP NR_027781.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MT1DP	NR_027781.1			downstream_gene_variant
MT1DP	NR_003658.2			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000463480.7			downstream_gene_variant		1
	ENST00000686953.2			downstream_gene_variant

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

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.811

Alfa AF: 0.830 Hom.: 14815

Bravo AF: 0.785

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs8044719; hg19: chr16-56678865;