rs5988291

Variant names:

• chrX-891455-T-G
• rs5988291

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 0.0896 in 152,070 control chromosomes in the GnomAD database, including 1,587 homozygotes. There are 6,570 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 0.090 (1587 hom., 6570 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

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 (AFR) allele frequency at 95% confidence interval = 0.258 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: 0.0894 AC: 13585 AN: 151952 Hom.: 1578 Cov.: 32 AF XY: 0.0880 AC XY: 6533 AN XY: 74204

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0896 AC: 13622 AN: 152070 Hom.: 1587 Cov.: 32 AF XY: 0.0884 AC XY: 6570 AN XY: 74332

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.00697

Gnomad4 OTH AF: 0.0730

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
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: rs5988291; hg19: chrX-852190;