rs2008165

Variant names:

• chrX-13030913-A-G
• rs2008165

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 0.53 (11033 hom., 17752 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• 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=-1.03).

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: 0.530 AC: 58707 AN: 110752 Hom.: 11026 Cov.: 22

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.526

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: 0.530 AC: 58753 AN: 110808 Hom.: 11033 Cov.: 22 AF XY: 0.537 AC XY: 17752 AN XY: 33062

African (AFR) AF: 0.544 AC: 16567 AN: 30466

American (AMR) AF: 0.673 AC: 7066 AN: 10499

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1244 AN: 2633

East Asian (EAS) AF: 0.632 AC: 2204 AN: 3486

South Asian (SAS) AF: 0.631 AC: 1674 AN: 2653

European-Finnish (FIN) AF: 0.573 AC: 3342 AN: 5831

Middle Eastern (MID) AF: 0.486 AC: 104 AN: 214

European-Non Finnish (NFE) AF: 0.483 AC: 25510 AN: 52822

Other (OTH) AF: 0.525 AC: 805 AN: 1533

Alfa AF: 0.525 Hom.: 13258

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.21
PhyloP100		-0.79

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: rs2008165;

hg19: chrX-13049032;