chrX-114583649-G-A

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;