X-853786-C-A

Variant names:

• chrX-853786-C-A
• 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 0.207 in 151,444 control chromosomes in the GnomAD database, including 3,430 homozygotes. There are 14,925 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 0.21 (3430 hom., 14925 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 (NFE) allele frequency at 95% confidence interval = 0.231 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: 0.208 AC: 31410 AN: 151326 Hom.: 3432 Cov.: 30 AF XY: 0.202 AC XY: 14907 AN XY: 73838

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.207 AC: 31414 AN: 151444 Hom.: 3430 Cov.: 30 AF XY: 0.202 AC XY: 14925 AN XY: 73966

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.60

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;