rs5959428

chrX-79690925-G-AchrX-79690925-G-CchrX-79690925-G-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 0.66 (18419 hom., 21223 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS2: High Homozygotes in GnomAd at 18430 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: 0.664 AC: 70664 AN: 106415 Hom.: 18430 Cov.: 21 AF XY: 0.656 AC XY: 21192 AN XY: 32303

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.684

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: 0.664 AC: 70677 AN: 106464 Hom.: 18419 Cov.: 21 AF XY: 0.656 AC XY: 21223 AN XY: 32364

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.683

Alfa AF: 0.747 Hom.: 20216

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.6
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: rs5959428; hg19: chrX-78946422;