rs950391

Positions:

• chrX-87199326-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 0.0434 in 110,684 control chromosomes in the GnomAD database, including 108 homozygotes. There are 1,282 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 0.043 (108 hom., 1282 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0781 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: 0.0432 AC: 4781 AN: 110635 Hom.: 107 Cov.: 22 AF XY: 0.0383 AC XY: 1267 AN XY: 33073

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.00292

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.000567

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0297

Gnomad NFE AF: 0.0337

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0434 AC: 4802 AN: 110684 Hom.: 108 Cov.: 22 AF XY: 0.0387 AC XY: 1282 AN XY: 33132

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.000569

Gnomad4 SAS AF: 0.0186

Gnomad4 FIN AF: 0.0194

Gnomad4 NFE AF: 0.0337

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.0348 Hom.: 1563

Bravo AF: 0.0452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950391; hg19: chrX-86454329;