X-93668425-C-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 0.54 (12011 hom., 17602 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd at 12004 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: 0.544 AC: 60088 AN: 110364 Hom.: 12004 Cov.: 22 AF XY: 0.538 AC XY: 17543 AN XY: 32590

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.526

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: 0.545 AC: 60155 AN: 110418 Hom.: 12011 Cov.: 22 AF XY: 0.539 AC XY: 17602 AN XY: 32654

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.524

Alfa AF: 0.483 Hom.: 47092

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.056
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5983240; hg19: chrX-92923424;