rs5987211

Positions:

• chrX-154110585-C-T

Variant summary

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

The variant allele was found at a frequency of 0.0891 in 111,814 control chromosomes in the GnomAD database, including 566 homozygotes. There are 2,679 hemizygotes in GnomAD. 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 0.089 (566 hom., 2679 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

MECP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.154110585C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MECP2	ENST00000631210.1	n.48-5547G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 9937 AN: 111762 Hom.: 563 Cov.: 22 AF XY: 0.0785 AC XY: 2666 AN XY: 33970

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.0418

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.0891 AC: 9965 AN: 111814 Hom.: 566 Cov.: 22 AF XY: 0.0787 AC XY: 2679 AN XY: 34032

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0393

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.0295

Gnomad4 FIN AF: 0.0481

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0911

Alfa AF: 0.0772 Hom.: 458

Bravo AF: 0.0973

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5987211; hg19: chrX-153376055;