chr8-97643979-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTDH	NM_178812.4	c.-528A>G		upstream_gene_variant		ENST00000336273.8	NP_848927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTDH	ENST00000336273.8	c.-528A>G		upstream_gene_variant		1	NM_178812.4	ENSP00000338235.3
ENSG00000287654	ENST00000659172.1	n.-98T>C		upstream_gene_variant

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

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.457

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.51
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

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