rs381365

Variant names:

• chrX-146667390-T-G
• rs381365

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 0.86 (28961 hom., 27455 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.856 AC: 94158 AN: 110000 Hom.: 28969 Cov.: 22

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.853

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: 0.856 AC: 94193 AN: 110050 Hom.: 28961 Cov.: 22 AF XY: 0.850 AC XY: 27455 AN XY: 32316

African (AFR) AF: 0.972 AC: 29437 AN: 30286

American (AMR) AF: 0.789 AC: 8123 AN: 10297

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 1899 AN: 2628

East Asian (EAS) AF: 0.668 AC: 2299 AN: 3443

South Asian (SAS) AF: 0.709 AC: 1837 AN: 2591

European-Finnish (FIN) AF: 0.827 AC: 4793 AN: 5794

Middle Eastern (MID) AF: 0.884 AC: 183 AN: 207

European-Non Finnish (NFE) AF: 0.833 AC: 43819 AN: 52632

Other (OTH) AF: 0.844 AC: 1263 AN: 1496

Alfa AF: 0.832 Hom.: 109448

Bravo AF: 0.859

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.42
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs381365; hg19: chrX-145748908;