rs5988291

chrX-891455-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;