X-147512898-A-T

Variant names:

• chrX-147512898-A-T
• rs1203029

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 0.49 (3164 hom., 6887 hem., cov: 2)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• 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=-1.04).

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: 0.487 AC: 23200 AN: 47591 Hom.: 3158 Cov.: 2

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.485

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.457

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: 0.488 AC: 23219 AN: 47613 Hom.: 3164 Cov.: 2 AF XY: 0.487 AC XY: 6887 AN XY: 14133

African (AFR) AF: 0.466 AC: 7315 AN: 15683

American (AMR) AF: 0.357 AC: 1471 AN: 4116

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 435 AN: 1030

East Asian (EAS) AF: 0.445 AC: 412 AN: 926

South Asian (SAS) AF: 0.419 AC: 522 AN: 1245

European-Finnish (FIN) AF: 0.615 AC: 1251 AN: 2034

Middle Eastern (MID) AF: 0.484 AC: 31 AN: 64

European-Non Finnish (NFE) AF: 0.522 AC: 11259 AN: 21577

Other (OTH) AF: 0.459 AC: 278 AN: 606

Alfa AF: 0.651 Hom.: 4629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1203029; hg19: chrX-146594416;