X-44795709-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 0.58 (13525 hom., 18531 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BS2: High Homozygotes in GnomAd at 13518 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: 0.580 AC: 63516 AN: 109589 Hom.: 13518 Cov.: 22 AF XY: 0.580 AC XY: 18493 AN XY: 31887

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.573

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: 0.580 AC: 63551 AN: 109645 Hom.: 13525 Cov.: 22 AF XY: 0.580 AC XY: 18531 AN XY: 31953

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.569

Alfa AF: 0.640 Hom.: 69546

Bravo AF: 0.580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.27
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs548996; hg19: chrX-44654955;