rs5920197

Positions:

• chrX-146526282-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.289 in 111,424 control chromosomes in the GnomAD database, including 4,149 homozygotes. There are 9,294 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 0.29 (4149 hom., 9294 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 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: 0.289 AC: 32213 AN: 111370 Hom.: 4153 Cov.: 23 AF XY: 0.277 AC XY: 9290 AN XY: 33586

Gnomad AFR AF: 0.0979

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.289 AC: 32197 AN: 111424 Hom.: 4149 Cov.: 23 AF XY: 0.276 AC XY: 9294 AN XY: 33650

Gnomad4 AFR AF: 0.0978

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.298

Alfa AF: 0.367 Hom.: 8121

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	10
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: rs5920197; hg19: chrX-145607800;