rs7890586

Variant names:

• chrX-100582827-G-A
• rs7890586

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 0.226 in 110,481 control chromosomes in the GnomAD database, including 2,760 homozygotes. There are 7,060 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 0.23 (2760 hom., 7060 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.226 AC: 24917 AN: 110427 Hom.: 2757 Cov.: 22 AF XY: 0.215 AC XY: 7051 AN XY: 32755

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.226 AC: 24932 AN: 110481 Hom.: 2760 Cov.: 22 AF XY: 0.215 AC XY: 7060 AN XY: 32819

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.224

Alfa AF: 0.186 Hom.: 2848

Bravo AF: 0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7890586; hg19: chrX-99837824;