chrX-122971702-A-T

Variant names:

• chrX-122971702-A-T
• rs1293524

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 0.90 (31586 hom., 28708 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.897 AC: 98532 AN: 109833 Hom.: 31593 Cov.: 22 AF XY: 0.894 AC XY: 28648 AN XY: 32043

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.894

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: 0.897 AC: 98579 AN: 109884 Hom.: 31586 Cov.: 22 AF XY: 0.894 AC XY: 28708 AN XY: 32104

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.891

Alfa AF: 0.897 Hom.: 7935

Bravo AF: 0.890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1293524; hg19: chrX-122105555;