chrX-50919299-C-T

Variant names:

• chrX-50919299-C-T
• rs2382663

Variant summary

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

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 0.32 (2632 hom., 4323 hem., cov: 14)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 21729 AN: 68337 Hom.: 2634 Cov.: 14

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.318 AC: 21717 AN: 68351 Hom.: 2632 Cov.: 14 AF XY: 0.325 AC XY: 4323 AN XY: 13307

African (AFR) AF: 0.103 AC: 1572 AN: 15202

American (AMR) AF: 0.306 AC: 1568 AN: 5118

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 792 AN: 1999

East Asian (EAS) AF: 0.0603 AC: 110 AN: 1824

South Asian (SAS) AF: 0.239 AC: 225 AN: 940

European-Finnish (FIN) AF: 0.462 AC: 1313 AN: 2840

Middle Eastern (MID) AF: 0.460 AC: 64 AN: 139

European-Non Finnish (NFE) AF: 0.397 AC: 15439 AN: 38871

Other (OTH) AF: 0.307 AC: 268 AN: 872

Alfa AF: 0.243 Hom.: 7153

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.50
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2382663; hg19: chrX-50662299;