rs321029

chrX-78328249-A-G

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 0.78 (24349 hom., 24253 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High Homozygotes in GnomAd at 24357 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: 0.781 AC: 85329 AN: 109229 Hom.: 24357 Cov.: 21 AF XY: 0.769 AC XY: 24200 AN XY: 31489

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.754

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: 0.781 AC: 85368 AN: 109286 Hom.: 24349 Cov.: 21 AF XY: 0.769 AC XY: 24253 AN XY: 31556

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.751

Alfa AF: 0.781 Hom.: 7867

Bravo AF: 0.779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.6
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs321029; hg19: chrX-77583746;