X-13025884-A-G

Variant names:

• chrX-13025884-A-G
• rs4830819

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 0.50 (9803 hom., 16178 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• 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=-1.05).

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: 0.497 AC: 54597 AN: 109953 Hom.: 9797 Cov.: 22

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.497

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: 0.497 AC: 54621 AN: 110006 Hom.: 9803 Cov.: 22 AF XY: 0.501 AC XY: 16178 AN XY: 32306

African (AFR) AF: 0.429 AC: 12970 AN: 30244

American (AMR) AF: 0.658 AC: 6773 AN: 10288

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1262 AN: 2624

East Asian (EAS) AF: 0.632 AC: 2195 AN: 3472

South Asian (SAS) AF: 0.632 AC: 1644 AN: 2601

European-Finnish (FIN) AF: 0.566 AC: 3244 AN: 5732

Middle Eastern (MID) AF: 0.491 AC: 106 AN: 216

European-Non Finnish (NFE) AF: 0.483 AC: 25436 AN: 52645

Other (OTH) AF: 0.497 AC: 752 AN: 1513

Alfa AF: 0.505 Hom.: 37497

Bravo AF: 0.512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs4830819; hg19: chrX-13044003;