rs1926025

Variant names:

• chrX-46359554-G-T
• rs1926025

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 0.91 (32369 hom., 29533 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• 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=-0.97).

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: 0.908 AC: 99999 AN: 110153 Hom.: 32380 Cov.: 22

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.918

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: 0.908 AC: 100025 AN: 110201 Hom.: 32369 Cov.: 22 AF XY: 0.911 AC XY: 29533 AN XY: 32433

African (AFR) AF: 0.749 AC: 22610 AN: 30183

American (AMR) AF: 0.884 AC: 9056 AN: 10250

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 2600 AN: 2636

East Asian (EAS) AF: 0.961 AC: 3358 AN: 3496

South Asian (SAS) AF: 0.938 AC: 2422 AN: 2582

European-Finnish (FIN) AF: 0.988 AC: 5660 AN: 5728

Middle Eastern (MID) AF: 0.931 AC: 202 AN: 217

European-Non Finnish (NFE) AF: 0.984 AC: 52077 AN: 52926

Other (OTH) AF: 0.919 AC: 1381 AN: 1503

Alfa AF: 0.935 Hom.: 10399

Bravo AF: 0.891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.54
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1926025; hg19: chrX-46218989;