rs5964577

Variant names:

• chrX-66951649-T-A
• rs5964577

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 3 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.652 AC: 71923 AN: 110289 Hom.: 20437 Cov.: 23

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

African (AFR) AF: 0.138 AC: 4238 AN: 30701

American (AMR) AF: 0.833 AC: 8491 AN: 10193

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 2416 AN: 2617

East Asian (EAS) AF: 0.998 AC: 3473 AN: 3480

South Asian (SAS) AF: 0.918 AC: 2358 AN: 2568

European-Finnish (FIN) AF: 0.825 AC: 4718 AN: 5721

Middle Eastern (MID) AF: 0.757 AC: 162 AN: 214

European-Non Finnish (NFE) AF: 0.843 AC: 44391 AN: 52660

Other (OTH) AF: 0.702 AC: 1058 AN: 1507

Alfa AF: 0.738 Hom.: 6295

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.37
DANN	Benign	0.33
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs5964577; hg19: chrX-66171491;