rs1573906

chrX-86880585-T-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 0.147 in 111,002 control chromosomes in the GnomAD database, including 1,100 homozygotes. There are 4,769 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 0.15 (1100 hom., 4769 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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 (AMR) allele frequency at 95% confidence interval = 0.298 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: 0.147 AC: 16337 AN: 110952 Hom.: 1096 Cov.: 23 AF XY: 0.143 AC XY: 4764 AN XY: 33376

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0556

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.147 AC: 16351 AN: 111002 Hom.: 1100 Cov.: 23 AF XY: 0.143 AC XY: 4769 AN XY: 33436

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.0778

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.158

Alfa AF: 0.134 Hom.: 753

Bravo AF: 0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.4
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1573906; hg19: chrX-86135588;