rs5945652

Variant names:

• chrX-51601443-G-A
• rs5945652

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;