rs177008

Variant names:

• chrX-125567397-A-G
• rs177008

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 (17259 hom., 21444 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• 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=-1.0).

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: 0.664 AC: 73116 AN: 110069 Hom.: 17259 Cov.: 22

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.671

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: 73155 AN: 110119 Hom.: 17259 Cov.: 22 AF XY: 0.662 AC XY: 21444 AN XY: 32401

African (AFR) AF: 0.600 AC: 18183 AN: 30321

American (AMR) AF: 0.697 AC: 7239 AN: 10383

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 1801 AN: 2622

East Asian (EAS) AF: 0.897 AC: 3073 AN: 3427

South Asian (SAS) AF: 0.724 AC: 1813 AN: 2505

European-Finnish (FIN) AF: 0.669 AC: 3870 AN: 5787

Middle Eastern (MID) AF: 0.720 AC: 154 AN: 214

European-Non Finnish (NFE) AF: 0.676 AC: 35609 AN: 52709

Other (OTH) AF: 0.672 AC: 999 AN: 1486

Alfa AF: 0.671 Hom.: 72602

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.43
PhyloP100		-1.4

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: rs177008;

hg19: chrX-124701246;