X-154026729-T-C

Variant names:

• chrX-154026729-T-C
• rs2734647
• NM_001110792.2:c.*3638A>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001110792.2(MECP2):​c.*3638A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.83 (28176 hom., 26347 hem., cov: 23)
  • Exomes 𝑓: 0.88 (77 hom. 131 hem.)
  • Failed GnomAD Quality Control
• Consequence: MECP2 NM_001110792.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.815
• Publications: 26 publications found

Genes affected

MECP2 (HGNC:6990): (methyl-CpG binding 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. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]

MECP2 Gene-Disease associations (from GenCC):

• chromosome Xq28 duplication syndrome

  Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
• Rett syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P
• severe neonatal-onset encephalopathy with microcephaly

  Inheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
• syndromic X-linked intellectual disability Lubs type

  Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
• atypical Rett syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• X-linked intellectual disability-psychosis-macroorchidism syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP6: Variant X-154026729-T-C is Benign according to our data. Variant chrX-154026729-T-C is described in ClinVar as [Benign]. Clinvar id is 3602016.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MECP2	NM_001110792.2	c.*3638A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000453960.7	NP_001104262.1
MECP2	NM_004992.4	c.*3638A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000303391.11	NP_004983.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MECP2	ENST00000453960.7	c.*3638A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_001110792.2	ENSP00000395535.2
MECP2	ENST00000303391.11	c.*3638A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_004992.4	ENSP00000301948.6
MECP2	ENST00000630151.3	c.*3638A>G		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000486089.2

Frequencies

GnomAD3 genomes AF: 0.827 AC: 91325 AN: 110435 Hom.: 28174 Cov.: 23

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.711

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.769

GnomAD4 exome AF: 0.875 AC: 309 AN: 353 Hom.: 77 Cov.: 0 AF XY: 0.868 AC XY: 131 AN XY: 151

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 1

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 1

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.890 AC: 267 AN: 300

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.829 AC: 34 AN: 41

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.827 AC: 91383 AN: 110489 Hom.: 28176 Cov.: 23 AF XY: 0.806 AC XY: 26347 AN XY: 32673

African (AFR) AF: 0.951 AC: 28844 AN: 30327

American (AMR) AF: 0.616 AC: 6434 AN: 10437

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2057 AN: 2631

East Asian (EAS) AF: 0.240 AC: 835 AN: 3478

South Asian (SAS) AF: 0.395 AC: 1038 AN: 2626

European-Finnish (FIN) AF: 0.857 AC: 4979 AN: 5810

Middle Eastern (MID) AF: 0.702 AC: 153 AN: 218

European-Non Finnish (NFE) AF: 0.857 AC: 45239 AN: 52787

Other (OTH) AF: 0.769 AC: 1152 AN: 1498

Alfa AF: 0.828 Hom.: 83561

Bravo AF: 0.814

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rett syndrome Benign:1

Dec 02, 2024

Centre for Population Genomics, CPG

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: curation

Based on the classification scheme defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders Specifications to the ACMG/AMP Variant Interpretation Guidelines VCEP 3.0, this variant is classified as benign. At least the following criteria are met: The allele frequency of this variant in at least one population in gnomAD is higher than the 0.03% threshold defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like Disorders VCEP 3.0 (BA1). The variant is observed in at least 2 individuals with no features of Rett Syndrome (BS2) (gnomAD homozygous count: 28253). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.81
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: rs2734647; hg19: chrX-153292180; COSMIC: COSV57653495; COSMIC: COSV57653495;