chrX-99251570-T-A

Variant names:

• chrX-99251570-T-A
• rs226729

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 1.0 (38701 hom., 31638 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.997 AC: 109189 AN: 109467 Hom.: 38706 Cov.: 21

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.998

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.999

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.997

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: 0.997 AC: 109244 AN: 109521 Hom.: 38701 Cov.: 21 AF XY: 0.998 AC XY: 31638 AN XY: 31707

African (AFR) AF: 1.00 AC: 30035 AN: 30047

American (AMR) AF: 0.998 AC: 10196 AN: 10212

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 2600 AN: 2626

East Asian (EAS) AF: 1.00 AC: 3431 AN: 3431

South Asian (SAS) AF: 0.999 AC: 2481 AN: 2484

European-Finnish (FIN) AF: 0.999 AC: 5629 AN: 5636

Middle Eastern (MID) AF: 1.00 AC: 215 AN: 215

European-Non Finnish (NFE) AF: 0.996 AC: 52474 AN: 52682

Other (OTH) AF: 0.997 AC: 1498 AN: 1503

Alfa AF: 0.997 Hom.: 9211

Bravo AF: 0.997

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs226729; hg19: chrX-98506568;