rs36208501

chrX-860031-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 0.061 (0 hom., 795 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.00 AC: 1782 AN: 29188 Hom.: 0 Cov.: 0 AF XY: 0.0588 AC XY: 793 AN XY: 13488 FAILED QC

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.0565

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0290

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.0727

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: AS_VQSR AF: 0.0611 AC: 1783 AN: 29182 Hom.: 0 Cov.: 0 AF XY: 0.0589 AC XY: 795 AN XY: 13500

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.0341

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0290

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.0723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36208501; hg19: chrX-820766; COSMIC: COSV55181719;