X-148299501-T-C

Position:

• chrX-148299501-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 0.54 (12748 hom., 18234 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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: 0.544 AC: 60330 AN: 110955 Hom.: 12741 Cov.: 23 AF XY: 0.549 AC XY: 18225 AN XY: 33211

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.553

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: 0.544 AC: 60339 AN: 111009 Hom.: 12748 Cov.: 23 AF XY: 0.548 AC XY: 18234 AN XY: 33275

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.555

Alfa AF: 0.583 Hom.: 14981

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2159767; hg19: chrX-147381021;