X-126667529-A-G

Variant names:

• chrX-126667529-A-G
• rs5929972

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 0.97 (36463 hom., 31800 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• 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=-1.04).

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: 0.968 AC: 107067 AN: 110598 Hom.: 36470 Cov.: 23

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.966

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.963

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: 0.968 AC: 107120 AN: 110653 Hom.: 36463 Cov.: 23 AF XY: 0.969 AC XY: 31800 AN XY: 32833

African (AFR) AF: 0.929 AC: 28216 AN: 30373

American (AMR) AF: 0.978 AC: 10172 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 2625 AN: 2639

East Asian (EAS) AF: 1.00 AC: 3486 AN: 3486

South Asian (SAS) AF: 0.988 AC: 2565 AN: 2595

European-Finnish (FIN) AF: 0.990 AC: 5789 AN: 5845

Middle Eastern (MID) AF: 0.968 AC: 210 AN: 217

European-Non Finnish (NFE) AF: 0.982 AC: 51966 AN: 52927

Other (OTH) AF: 0.963 AC: 1445 AN: 1500

Alfa AF: 0.974 Hom.: 25804

Bravo AF: 0.965

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5929972; hg19: chrX-125801512;