rs950391

Variant names:

• chrX-87199326-G-A
• rs950391

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;