rs2032468

Variant names:

• chrX-127976473-A-G
• rs2032468

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 0.80 (24859 hom., 25906 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• 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=-1.06).

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: 0.796 AC: 87863 AN: 110420 Hom.: 24870 Cov.: 22

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.798

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: 0.795 AC: 87877 AN: 110468 Hom.: 24859 Cov.: 22 AF XY: 0.792 AC XY: 25906 AN XY: 32694

African (AFR) AF: 0.724 AC: 21957 AN: 30337

American (AMR) AF: 0.712 AC: 7358 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2123 AN: 2634

East Asian (EAS) AF: 0.931 AC: 3236 AN: 3477

South Asian (SAS) AF: 0.816 AC: 2085 AN: 2554

European-Finnish (FIN) AF: 0.785 AC: 4580 AN: 5837

Middle Eastern (MID) AF: 0.840 AC: 179 AN: 213

European-Non Finnish (NFE) AF: 0.845 AC: 44673 AN: 52896

Other (OTH) AF: 0.800 AC: 1203 AN: 1504

Alfa AF: 0.823 Hom.: 131691

Bravo AF: 0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.29
PhyloP100		-1.9

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: rs2032468;

hg19: chrX-127110452;