rs5945652

Variant names:

• chrX-51601443-G-A
• rs5945652

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.269 AC: 29922 AN: 111355 Hom.: 3071 Cov.: 24

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

African (AFR) AF: 0.260 AC: 7988 AN: 30693

American (AMR) AF: 0.163 AC: 1718 AN: 10516

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 610 AN: 2643

East Asian (EAS) AF: 0.267 AC: 943 AN: 3532

South Asian (SAS) AF: 0.229 AC: 605 AN: 2643

European-Finnish (FIN) AF: 0.261 AC: 1565 AN: 6004

Middle Eastern (MID) AF: 0.163 AC: 35 AN: 215

European-Non Finnish (NFE) AF: 0.299 AC: 15829 AN: 52976

Other (OTH) AF: 0.246 AC: 374 AN: 1521

Alfa AF: 0.283 Hom.: 28563

Bravo AF: 0.260

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.60
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs5945652; hg19: chrX-51344295;