X-853786-C-T

Variant names:

• chrX-853786-C-T
• rs5946503

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 0.217 in 151,472 control chromosomes in the GnomAD database, including 3,901 homozygotes. There are 16,621 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 0.22 (3901 hom., 16621 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32850 AN: 151354 Hom.: 3888 Cov.: 30 AF XY: 0.225 AC XY: 16600 AN XY: 73850

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.217 AC: 32891 AN: 151472 Hom.: 3901 Cov.: 30 AF XY: 0.225 AC XY: 16621 AN XY: 73978

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946503; hg19: chrX-814521;