X-42995357-A-G

Variant names:

• chrX-42995357-A-G
• rs7881785

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 0.71 (19876 hom., 23674 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• 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=-0.96).

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: 0.711 AC: 78818 AN: 110922 Hom.: 19867 Cov.: 23

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.914

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.688

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: 0.711 AC: 78877 AN: 110973 Hom.: 19876 Cov.: 23 AF XY: 0.713 AC XY: 23674 AN XY: 33191

African (AFR) AF: 0.789 AC: 24105 AN: 30556

American (AMR) AF: 0.724 AC: 7581 AN: 10477

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 1626 AN: 2635

East Asian (EAS) AF: 0.914 AC: 3207 AN: 3507

South Asian (SAS) AF: 0.820 AC: 2162 AN: 2637

European-Finnish (FIN) AF: 0.730 AC: 4259 AN: 5837

Middle Eastern (MID) AF: 0.590 AC: 128 AN: 217

European-Non Finnish (NFE) AF: 0.649 AC: 34363 AN: 52924

Other (OTH) AF: 0.691 AC: 1041 AN: 1507

Alfa AF: 0.682 Hom.: 6645

Bravo AF: 0.718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.50
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs7881785; hg19: chrX-42854606;