rs5959428

Variant names:

• chrX-79690925-G-A
• rs5959428

Your query was ambiguous. Multiple possible variants found:

• chrX-79690925-G-A
• chrX-79690925-G-C
• chrX-79690925-G-T

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 0.66 (18419 hom., 21223 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.664 AC: 70664 AN: 106415 Hom.: 18430 Cov.: 21

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.684

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: 0.664 AC: 70677 AN: 106464 Hom.: 18419 Cov.: 21 AF XY: 0.656 AC XY: 21223 AN XY: 32364

African (AFR) AF: 0.396 AC: 11900 AN: 30030

American (AMR) AF: 0.552 AC: 5361 AN: 9705

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2100 AN: 2529

East Asian (EAS) AF: 0.634 AC: 2112 AN: 3332

South Asian (SAS) AF: 0.755 AC: 1933 AN: 2559

European-Finnish (FIN) AF: 0.811 AC: 4519 AN: 5575

Middle Eastern (MID) AF: 0.849 AC: 174 AN: 205

European-Non Finnish (NFE) AF: 0.814 AC: 41072 AN: 50429

Other (OTH) AF: 0.683 AC: 985 AN: 1443

Alfa AF: 0.717 Hom.: 29096

Bravo AF: 0.618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.70
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs5959428; hg19: chrX-78946422;