X-117469443-T-C

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 0.61 (15364 hom., 20345 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS2: High Homozygotes in GnomAd at 15360 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: 0.614 AC: 67883 AN: 110632 Hom.: 15360 Cov.: 23 AF XY: 0.617 AC XY: 20295 AN XY: 32872

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.491

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: 0.614 AC: 67935 AN: 110687 Hom.: 15364 Cov.: 23 AF XY: 0.618 AC XY: 20345 AN XY: 32937

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.610

Alfa AF: 0.520 Hom.: 39554

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040962; hg19: chrX-116603406;