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).

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: 0.487 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 v4.3

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;