rs498207

Variant names:

• chrX-114583649-G-A
• rs498207

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 (16963 hom., 20920 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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: 0.657 AC: 72044 AN: 109634 Hom.: 16974 Cov.: 22

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.689

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: 0.657 AC: 72046 AN: 109687 Hom.: 16963 Cov.: 22 AF XY: 0.654 AC XY: 20920 AN XY: 31993

African (AFR) AF: 0.626 AC: 18784 AN: 30029

American (AMR) AF: 0.653 AC: 6764 AN: 10360

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 1676 AN: 2629

East Asian (EAS) AF: 0.846 AC: 2897 AN: 3426

South Asian (SAS) AF: 0.595 AC: 1519 AN: 2552

European-Finnish (FIN) AF: 0.721 AC: 4125 AN: 5725

Middle Eastern (MID) AF: 0.637 AC: 137 AN: 215

European-Non Finnish (NFE) AF: 0.658 AC: 34576 AN: 52575

Other (OTH) AF: 0.690 AC: 1035 AN: 1500

Alfa AF: 0.649 Hom.: 26313

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
PhyloP100		1.0
PromoterAI		-0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs498207; hg19: chrX-113818116;