rs5945652

Positions:

• chrX-51601443-G-A

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 0.269 in 111,407 control chromosomes in the GnomAD database, including 3,070 homozygotes. There are 8,574 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 0.27 (3070 hom., 8574 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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: 0.269 AC: 29922 AN: 111355 Hom.: 3071 Cov.: 24 AF XY: 0.255 AC XY: 8568 AN XY: 33629

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.269 AC: 29917 AN: 111407 Hom.: 3070 Cov.: 24 AF XY: 0.255 AC XY: 8574 AN XY: 33689

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.246

Alfa AF: 0.290 Hom.: 21490

Bravo AF: 0.260

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
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: rs5945652; hg19: chrX-51344295;