rs5988300

Variant names:

• chrX-920268-A-G
• rs5988300

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 0.506 in 151,802 control chromosomes in the GnomAD database, including 20,093 homozygotes. There are 37,776 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 0.51 (20093 hom., 37776 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.506 AC: 76786 AN: 151684 Hom.: 20063 Cov.: 31 AF XY: 0.509 AC XY: 37687 AN XY: 74036

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76864 AN: 151802 Hom.: 20093 Cov.: 31 AF XY: 0.509 AC XY: 37776 AN XY: 74164

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.499

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.7
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988300; hg19: chrX-881003;