X-100510088-G-C

Position:

• chrX-100510088-G-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 0.63 (17441 hom., 19621 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.631 AC: 69440 AN: 110052 Hom.: 17439 Cov.: 22 AF XY: 0.606 AC XY: 19563 AN XY: 32284

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.604

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: 0.631 AC: 69494 AN: 110103 Hom.: 17441 Cov.: 22 AF XY: 0.607 AC XY: 19621 AN XY: 32345

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.602

Alfa AF: 0.354 Hom.: 1381

Bravo AF: 0.650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768198; hg19: chrX-99765085;