rs1034948

Variant names:

• chrX-30313232-A-G
• rs1034948

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 0.80 (25369 hom., 26290 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• 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=-0.68).

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: 0.802 AC: 88659 AN: 110580 Hom.: 25376 Cov.: 23

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.813

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: 0.802 AC: 88680 AN: 110634 Hom.: 25369 Cov.: 23 AF XY: 0.800 AC XY: 26290 AN XY: 32856

African (AFR) AF: 0.673 AC: 20445 AN: 30389

American (AMR) AF: 0.741 AC: 7669 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 2343 AN: 2642

East Asian (EAS) AF: 0.861 AC: 3032 AN: 3523

South Asian (SAS) AF: 0.863 AC: 2214 AN: 2565

European-Finnish (FIN) AF: 0.877 AC: 5102 AN: 5817

Middle Eastern (MID) AF: 0.821 AC: 179 AN: 218

European-Non Finnish (NFE) AF: 0.867 AC: 45914 AN: 52968

Other (OTH) AF: 0.807 AC: 1204 AN: 1492

Alfa AF: 0.842 Hom.: 125232

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.9
DANN	Benign	0.52
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1034948; hg19: chrX-30331349;