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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;