rs5969113

Variant names:

• chrX-87171885-C-T
• rs5969113

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.271 in 109,460 control chromosomes in the GnomAD database, including 3,240 homozygotes. There are 8,531 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 0.27 (3240 hom., 8531 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 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: 0.271 AC: 29697 AN: 109421 Hom.: 3240 Cov.: 22

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.271 AC: 29693 AN: 109460 Hom.: 3240 Cov.: 22 AF XY: 0.268 AC XY: 8531 AN XY: 31814

Gnomad4 AFR AF: 0.152 AC: 0.152065 AN: 0.152065

Gnomad4 AMR AF: 0.288 AC: 0.288352 AN: 0.288352

Gnomad4 ASJ AF: 0.305 AC: 0.304729 AN: 0.304729

Gnomad4 EAS AF: 0.668 AC: 0.667742 AN: 0.667742

Gnomad4 SAS AF: 0.284 AC: 0.284215 AN: 0.284215

Gnomad4 FIN AF: 0.360 AC: 0.36043 AN: 0.36043

Gnomad4 NFE AF: 0.299 AC: 0.299297 AN: 0.299297

Gnomad4 OTH AF: 0.301 AC: 0.30109 AN: 0.30109

Alfa AF: 0.285 Hom.: 10127

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5969113; hg19: chrX-86426888;