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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;