X-42962599-G-A

Variant names:

• chrX-42962599-G-A
• rs996106

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 0.54 (11563 hom., 17348 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• 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: 0.535 AC: 58849 AN: 109983 Hom.: 11557 Cov.: 22

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.556

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: 0.535 AC: 58877 AN: 110035 Hom.: 11563 Cov.: 22 AF XY: 0.536 AC XY: 17348 AN XY: 32347

African (AFR) AF: 0.376 AC: 11400 AN: 30321

American (AMR) AF: 0.665 AC: 6858 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1395 AN: 2620

East Asian (EAS) AF: 0.716 AC: 2495 AN: 3484

South Asian (SAS) AF: 0.530 AC: 1359 AN: 2562

European-Finnish (FIN) AF: 0.635 AC: 3652 AN: 5748

Middle Eastern (MID) AF: 0.616 AC: 130 AN: 211

European-Non Finnish (NFE) AF: 0.581 AC: 30540 AN: 52587

Other (OTH) AF: 0.556 AC: 838 AN: 1506

Alfa AF: 0.573 Hom.: 34505

Bravo AF: 0.538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs996106; hg19: chrX-42821848;