rs950391

Variant names:

• chrX-87199326-G-A
• rs950391

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 0.0434 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0808 AC: 2467 AN: 30543

American (AMR) AF: 0.0291 AC: 303 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 34 AN: 2625

East Asian (EAS) AF: 0.000569 AC: 2 AN: 3515

South Asian (SAS) AF: 0.0186 AC: 49 AN: 2639

European-Finnish (FIN) AF: 0.0194 AC: 116 AN: 5977

Middle Eastern (MID) AF: 0.0326 AC: 7 AN: 215

European-Non Finnish (NFE) AF: 0.0337 AC: 1773 AN: 52586

Other (OTH) AF: 0.0326 AC: 49 AN: 1503

Alfa AF: 0.0361 Hom.: 2320

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
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs950391; hg19: chrX-86454329;