rs1005295

chrX-80086889-T-CchrX-80086889-T-G

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 0.199 in 111,522 control chromosomes in the GnomAD database, including 1,598 homozygotes. There are 6,794 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 0.20 (1598 hom., 6794 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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: 0.199 AC: 22157 AN: 111473 Hom.: 1600 Cov.: 23 AF XY: 0.202 AC XY: 6792 AN XY: 33665

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.181

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.199 AC: 22152 AN: 111522 Hom.: 1598 Cov.: 23 AF XY: 0.201 AC XY: 6794 AN XY: 33724

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.183

Alfa AF: 0.204 Hom.: 9379

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.0010
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1005295; hg19: chrX-79342388;