rs5964577

Positions:

• chrX-66951649-T-A
• chrX-66951649-T-C
• chrX-66951649-T-G

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 0.65 (20427 hom., 21529 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66951649T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 71923 AN: 110289 Hom.: 20437 Cov.: 23 AF XY: 0.661 AC XY: 21518 AN XY: 32549

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.762

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.700

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: 0.652 AC: 71908 AN: 110340 Hom.: 20427 Cov.: 23 AF XY: 0.660 AC XY: 21529 AN XY: 32610

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.702

Alfa AF: 0.738 Hom.: 6295

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5964577; hg19: chrX-66171491;