rs5990890

Variant names:

• chrX-20575680-T-G
• rs5990890

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 0.23 in 110,958 control chromosomes in the GnomAD database, including 2,946 homozygotes. There are 7,458 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 (2946 hom., 7458 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.866

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 = 0.437 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: 0.230 AC: 25486 AN: 110903 Hom.: 2942 Cov.: 22 AF XY: 0.224 AC XY: 7434 AN XY: 33123

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.230 AC: 25517 AN: 110958 Hom.: 2946 Cov.: 22 AF XY: 0.225 AC XY: 7458 AN XY: 33188

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.234

Alfa AF: 0.191 Hom.: 1251

Bravo AF: 0.246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
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: rs5990890; hg19: chrX-20593798;