rs239748

Positions:

• chrX-18865240-T-C

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 0.65 (18619 hom., 20392 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

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: 0.646 AC: 70679 AN: 109374 Hom.: 18628 Cov.: 22 AF XY: 0.644 AC XY: 20379 AN XY: 31664

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.656

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: 0.646 AC: 70668 AN: 109431 Hom.: 18619 Cov.: 22 AF XY: 0.643 AC XY: 20392 AN XY: 31731

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.653

Alfa AF: 0.774 Hom.: 21693

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs239748; hg19: chrX-18883358;