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
• Publications: 0 publications found

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.152 AC: 4598 AN: 30237

American (AMR) AF: 0.288 AC: 2936 AN: 10182

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 799 AN: 2622

East Asian (EAS) AF: 0.668 AC: 2277 AN: 3410

South Asian (SAS) AF: 0.284 AC: 731 AN: 2572

European-Finnish (FIN) AF: 0.360 AC: 2013 AN: 5585

Middle Eastern (MID) AF: 0.198 AC: 42 AN: 212

European-Non Finnish (NFE) AF: 0.299 AC: 15711 AN: 52493

Other (OTH) AF: 0.301 AC: 442 AN: 1468

Alfa AF: 0.285 Hom.: 10127

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs5969113; hg19: chrX-86426888;