rs7889321

chrX-50932928-A-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 0.166 in 111,227 control chromosomes in the GnomAD database, including 2,717 homozygotes. There are 5,070 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 0.17 (2717 hom., 5070 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.166 AC: 18423 AN: 111171 Hom.: 2715 Cov.: 23 AF XY: 0.151 AC XY: 5061 AN XY: 33419

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.0261

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0508

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0130

Gnomad MID AF: 0.0932

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.166 AC: 18436 AN: 111227 Hom.: 2717 Cov.: 23 AF XY: 0.151 AC XY: 5070 AN XY: 33485

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.0810

Gnomad4 ASJ AF: 0.0508

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0130

Gnomad4 NFE AF: 0.0390

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0580 Hom.: 1749

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7889321; hg19: chrX-50675928;