X-853959-C-T

Variant names:

• chrX-853959-C-T
• rs5988279

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 0.311 in 151,480 control chromosomes in the GnomAD database, including 9,083 homozygotes. There are 23,148 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 0.31 (9083 hom., 23148 hem., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 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: 0.311 AC: 47148 AN: 151362 Hom.: 9071 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.311 AC: 47180 AN: 151480 Hom.: 9083 Cov.: 33 AF XY: 0.313 AC XY: 23148 AN XY: 73938

African (AFR) AF: 0.535 AC: 22117 AN: 41372

American (AMR) AF: 0.252 AC: 3830 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3464

East Asian (EAS) AF: 0.456 AC: 2328 AN: 5100

South Asian (SAS) AF: 0.341 AC: 1631 AN: 4776

European-Finnish (FIN) AF: 0.257 AC: 2697 AN: 10486

Middle Eastern (MID) AF: 0.209 AC: 58 AN: 278

European-Non Finnish (NFE) AF: 0.197 AC: 13346 AN: 67802

Other (OTH) AF: 0.245 AC: 515 AN: 2100

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs5988279; hg19: chrX-814694;