rs1573906

Variant names:

• chrX-86880585-T-C
• rs1573906

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;