rs5988460

Positions:

• chrX-890459-A-G
• chrX-890459-A-T

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 0.394 in 151,986 control chromosomes in the GnomAD database, including 15,310 homozygotes. There are 29,819 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 0.39 (15310 hom., 29819 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.394 AC: 59794 AN: 151868 Hom.: 15272 Cov.: 32 AF XY: 0.401 AC XY: 29715 AN XY: 74152

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.394 AC: 59883 AN: 151986 Hom.: 15310 Cov.: 32 AF XY: 0.401 AC XY: 29819 AN XY: 74280

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.358

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.094
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988460; hg19: chrX-851194;