NM_178812.4:c.-528A>G

Variant names:

• chr8-97643979-A-G
• rs2512449
• NM_178812.4:c.-528A>G

Variant summary

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

The NM_178812.4(MTDH):​c.-528A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 150,000 control chromosomes in the GnomAD database, including 20,037 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 0.48 (20037 hom., cov: 26)
• Consequence: MTDH NM_178812.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 1 publications found

Genes affected

MTDH (HGNC:29608): (metadherin) Enables NF-kappaB binding activity; double-stranded RNA binding activity; and transcription coactivator activity. Involved in several processes, including lipopolysaccharide-mediated signaling pathway; positive regulation of intracellular signal transduction; and regulation of transcription, DNA-templated. Located in endoplasmic reticulum; nuclear lumen; and perinuclear region of cytoplasm. Implicated in hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000287654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178812.4. 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
	MTDH	NM_178812.4	MANE Select	c.-528A>G		upstream_gene	N/A	NP_848927.2
	MTDH	NM_001363137.1		c.-528A>G		upstream_gene	N/A	NP_001350066.1
	MTDH	NM_001363136.1		c.-528A>G		upstream_gene	N/A	NP_001350065.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTDH	ENST00000336273.8	TSL:1 MANE Select	c.-528A>G		upstream_gene	N/A	ENSP00000338235.3
	MTDH	ENST00000887774.1		c.-528A>G		upstream_gene	N/A	ENSP00000557833.1
	MTDH	ENST00000915586.1		c.-528A>G		upstream_gene	N/A	ENSP00000585645.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 71897 AN: 149886 Hom.: 19988 Cov.: 26

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.480 AC: 71999 AN: 150000 Hom.: 20037 Cov.: 26 AF XY: 0.482 AC XY: 35216 AN XY: 73112

African (AFR) AF: 0.767 AC: 31451 AN: 41028

American (AMR) AF: 0.455 AC: 6835 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1354 AN: 3456

East Asian (EAS) AF: 0.631 AC: 3166 AN: 5014

South Asian (SAS) AF: 0.528 AC: 2480 AN: 4694

European-Finnish (FIN) AF: 0.333 AC: 3371 AN: 10116

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 21919 AN: 67380

Other (OTH) AF: 0.457 AC: 952 AN: 2084

Alfa AF: 0.258 Hom.: 649

Bravo AF: 0.497

Asia WGS AF: 0.593 AC: 2044 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.51
DANN	Benign	0.40
PhyloP100		-2.4
PromoterAI		0.054	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2512449; hg19: chr8-98656207; COSMIC: COSV60345003;