rs1381733

Variant names:

• chrX-100014722-G-A
• rs1381733

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 0.64 (16749 hom., 21060 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.638 AC: 70346 AN: 110211 Hom.: 16750 Cov.: 23

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.656

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: 0.638 AC: 70368 AN: 110264 Hom.: 16749 Cov.: 23 AF XY: 0.646 AC XY: 21060 AN XY: 32576

African (AFR) AF: 0.382 AC: 11603 AN: 30372

American (AMR) AF: 0.724 AC: 7475 AN: 10322

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 1642 AN: 2637

East Asian (EAS) AF: 0.999 AC: 3499 AN: 3504

South Asian (SAS) AF: 0.888 AC: 2261 AN: 2546

European-Finnish (FIN) AF: 0.746 AC: 4290 AN: 5752

Middle Eastern (MID) AF: 0.521 AC: 111 AN: 213

European-Non Finnish (NFE) AF: 0.718 AC: 37898 AN: 52755

Other (OTH) AF: 0.661 AC: 981 AN: 1485

Alfa AF: 0.710 Hom.: 22080

Bravo AF: 0.630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.70
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1381733; hg19: chrX-99269720;