X-138206413-A-T

Variant names:

• chrX-138206413-A-T
• rs398262

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.72 (20340 hom., 22906 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

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: 0.715 AC: 78556 AN: 109820 Hom.: 20344 Cov.: 23

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.692

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.715 AC: 78593 AN: 109872 Hom.: 20340 Cov.: 23 AF XY: 0.712 AC XY: 22906 AN XY: 32190

African (AFR) AF: 0.615 AC: 18602 AN: 30224

American (AMR) AF: 0.636 AC: 6519 AN: 10249

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 1775 AN: 2630

East Asian (EAS) AF: 0.489 AC: 1688 AN: 3451

South Asian (SAS) AF: 0.860 AC: 2194 AN: 2551

European-Finnish (FIN) AF: 0.799 AC: 4571 AN: 5718

Middle Eastern (MID) AF: 0.689 AC: 146 AN: 212

European-Non Finnish (NFE) AF: 0.789 AC: 41530 AN: 52657

Other (OTH) AF: 0.693 AC: 1039 AN: 1499

Alfa AF: 0.754 Hom.: 6217

Bravo AF: 0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.63
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs398262; hg19: chrX-137288572;