X-3303783-G-A

Variant names:

• chrX-3303783-G-A
• rs1527036

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 0.62 (15185 hom., 18972 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• 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=-0.91).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.620 AC: 67227 AN: 108448 Hom.: 15197 Cov.: 21

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.633

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: 0.620 AC: 67226 AN: 108501 Hom.: 15185 Cov.: 21 AF XY: 0.612 AC XY: 18972 AN XY: 30999

African (AFR) AF: 0.523 AC: 15657 AN: 29911

American (AMR) AF: 0.634 AC: 6449 AN: 10177

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 1736 AN: 2599

East Asian (EAS) AF: 0.728 AC: 2444 AN: 3358

South Asian (SAS) AF: 0.644 AC: 1557 AN: 2418

European-Finnish (FIN) AF: 0.682 AC: 3817 AN: 5599

Middle Eastern (MID) AF: 0.673 AC: 140 AN: 208

European-Non Finnish (NFE) AF: 0.653 AC: 34034 AN: 52091

Other (OTH) AF: 0.626 AC: 929 AN: 1483

Alfa AF: 0.642 Hom.: 6082

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1527036; hg19: chrX-3221824;