18-54175426-C-T

Variant names:

• chr18-54175426-C-T
• rs656923
• NM_003927.5:c.841-9260G>A

Variant summary

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

The NM_003927.5(MBD2):​c.841-9260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,248 control chromosomes in the GnomAD database, including 55,869 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 0.85 (55869 hom., cov: 31)
• Consequence: MBD2 NM_003927.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 1 publications found

Genes affected

MBD2 (HGNC:6917): (methyl-CpG binding domain protein 2) DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that the this protein functions as a demethylase to activate transcription, as DNA methylation causes gene silencing. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBD2	NM_003927.5	c.841-9260G>A		intron_variant	Intron 3 of 6	ENST00000256429.8	NP_003918.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBD2	ENST00000256429.8	c.841-9260G>A		intron_variant	Intron 3 of 6	1	NM_003927.5	ENSP00000256429.3
MBD2	ENST00000578272.1	n.*68-9260G>A		intron_variant	Intron 3 of 5	5		ENSP00000462393.1

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129792 AN: 152128 Hom.: 55811 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.853 AC: 129910 AN: 152248 Hom.: 55869 Cov.: 31 AF XY: 0.854 AC XY: 63591 AN XY: 74424

African (AFR) AF: 0.960 AC: 39892 AN: 41566

American (AMR) AF: 0.804 AC: 12297 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5161 AN: 5178

South Asian (SAS) AF: 0.782 AC: 3776 AN: 4826

European-Finnish (FIN) AF: 0.827 AC: 8765 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54295 AN: 67998

Other (OTH) AF: 0.843 AC: 1783 AN: 2114

Alfa AF: 0.829 Hom.: 20186

Bravo AF: 0.855

Asia WGS AF: 0.906 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.43
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

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: rs656923; hg19: chr18-51701796;