rs989345

Positions:

• chrX-67081192-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 (20451 hom., 21306 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.658 AC: 72065 AN: 109582 Hom.: 20459 Cov.: 22 AF XY: 0.669 AC XY: 21298 AN XY: 31856

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.762

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.705

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: 0.657 AC: 72050 AN: 109624 Hom.: 20451 Cov.: 22 AF XY: 0.668 AC XY: 21306 AN XY: 31908

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.706

Alfa AF: 0.829 Hom.: 96554

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs989345; hg19: chrX-66301034;