chrX-84249323-C-T

Variant names:

• chrX-84249323-C-T
• rs765076

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 0.55 (12040 hom., 16450 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.555 AC: 59450 AN: 107208 Hom.: 12048 Cov.: 20

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.562

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.558

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: 0.555 AC: 59480 AN: 107250 Hom.: 12040 Cov.: 20 AF XY: 0.552 AC XY: 16450 AN XY: 29774

African (AFR) AF: 0.557 AC: 16412 AN: 29472

American (AMR) AF: 0.654 AC: 6517 AN: 9962

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1381 AN: 2593

East Asian (EAS) AF: 0.760 AC: 2565 AN: 3376

South Asian (SAS) AF: 0.571 AC: 1350 AN: 2366

European-Finnish (FIN) AF: 0.432 AC: 2232 AN: 5165

Middle Eastern (MID) AF: 0.544 AC: 111 AN: 204

European-Non Finnish (NFE) AF: 0.532 AC: 27686 AN: 51993

Other (OTH) AF: 0.555 AC: 806 AN: 1451

Alfa AF: 0.541 Hom.: 70998

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs765076; hg19: chrX-83504331;