X-126667529-A-G

Position:

• chrX-126667529-A-G

Variant summary

Our verdict is Likely benign. Variant got -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 0.97 (36463 hom., 31800 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.968 AC: 107067 AN: 110598 Hom.: 36470 Cov.: 23 AF XY: 0.968 AC XY: 31735 AN XY: 32768

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.966

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.963

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: 0.968 AC: 107120 AN: 110653 Hom.: 36463 Cov.: 23 AF XY: 0.969 AC XY: 31800 AN XY: 32833

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.963

Alfa AF: 0.975 Hom.: 20321

Bravo AF: 0.965

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5929972; hg19: chrX-125801512;