rs1151737

chrX-123011389-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.57 (13165 hom., 18100 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS2: High Homozygotes in GnomAd at 13157 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 62644 AN: 110606 Hom.: 13157 Cov.: 23 AF XY: 0.550 AC XY: 18074 AN XY: 32846

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.578

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: 0.566 AC: 62677 AN: 110666 Hom.: 13165 Cov.: 23 AF XY: 0.550 AC XY: 18100 AN XY: 32916

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.579

Alfa AF: 0.600 Hom.: 4556

Bravo AF: 0.555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.081
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1151737; hg19: chrX-122145242;