rs5909876

chrX-122088395-G-AchrX-122088395-G-C

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 0.25 in 110,783 control chromosomes in the GnomAD database, including 3,039 homozygotes. There are 8,433 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 0.25 (3039 hom., 8433 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 27662 AN: 110730 Hom.: 3040 Cov.: 23 AF XY: 0.255 AC XY: 8428 AN XY: 33004

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.250 AC: 27659 AN: 110783 Hom.: 3039 Cov.: 23 AF XY: 0.255 AC XY: 8433 AN XY: 33067

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.243

Alfa AF: 0.257 Hom.: 2547

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.48
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5909876; hg19: chrX-121222248;