rs5968255

chrX-83999684-T-CchrX-83999684-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 0.127 in 111,247 control chromosomes in the GnomAD database, including 873 homozygotes. There are 4,257 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 0.13 (873 hom., 4257 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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: 0.127 AC: 14155 AN: 111188 Hom.: 872 Cov.: 22 AF XY: 0.127 AC XY: 4255 AN XY: 33416

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.0966

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.127 AC: 14160 AN: 111247 Hom.: 873 Cov.: 22 AF XY: 0.127 AC XY: 4257 AN XY: 33485

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.116

Alfa AF: 0.129 Hom.: 9400

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5968255; hg19: chrX-83254692;