rs6529954

Variant names:

• chrX-4266308-A-G
• rs6529954

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 0.59 (15783 hom., 17926 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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: 0.594 AC: 65007 AN: 109380 Hom.: 15779 Cov.: 21

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.567

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: 0.594 AC: 65048 AN: 109435 Hom.: 15783 Cov.: 21 AF XY: 0.565 AC XY: 17926 AN XY: 31753

African (AFR) AF: 0.897 AC: 26908 AN: 30001

American (AMR) AF: 0.440 AC: 4458 AN: 10129

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1400 AN: 2618

East Asian (EAS) AF: 0.186 AC: 646 AN: 3482

South Asian (SAS) AF: 0.364 AC: 927 AN: 2550

European-Finnish (FIN) AF: 0.439 AC: 2503 AN: 5699

Middle Eastern (MID) AF: 0.569 AC: 123 AN: 216

European-Non Finnish (NFE) AF: 0.511 AC: 26891 AN: 52583

Other (OTH) AF: 0.560 AC: 832 AN: 1487

Alfa AF: 0.545 Hom.: 20232

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.34
PhyloP100		-0.94

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6529954;

hg19: chrX-4184349;