rs5906754

Positions:

• chrX-49203767-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 0.516 in 110,102 control chromosomes in the GnomAD database, including 11,948 homozygotes. There are 16,526 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 0.52 (11948 hom., 16526 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.516 AC: 56774 AN: 110047 Hom.: 11956 Cov.: 22 AF XY: 0.511 AC XY: 16505 AN XY: 32311

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.516 AC: 56764 AN: 110102 Hom.: 11948 Cov.: 22 AF XY: 0.510 AC XY: 16526 AN XY: 32376

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.547

Alfa AF: 0.568 Hom.: 3343

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.8

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5906754; hg19: chrX-49060227;