rs5945971

chrX-103328477-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 0.67 (18704 hom., 21188 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

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 18701 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: 0.671 AC: 73563 AN: 109690 Hom.: 18701 Cov.: 22 AF XY: 0.661 AC XY: 21132 AN XY: 31992

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.552

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.644

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: 0.671 AC: 73614 AN: 109739 Hom.: 18704 Cov.: 22 AF XY: 0.661 AC XY: 21188 AN XY: 32051

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.644

Alfa AF: 0.617 Hom.: 4848

Bravo AF: 0.692

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.54
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945971; hg19: chrX-102583405;