chrX-15882205-A-G

Variant names:

• chrX-15882205-A-G
• rs798159

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 0.81 (25918 hom., 26915 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: 0.811 AC: 89817 AN: 110804 Hom.: 25913 Cov.: 23

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.746

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.820

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: 0.811 AC: 89880 AN: 110857 Hom.: 25918 Cov.: 23 AF XY: 0.814 AC XY: 26915 AN XY: 33051

African (AFR) AF: 0.948 AC: 28906 AN: 30494

American (AMR) AF: 0.878 AC: 9166 AN: 10436

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 1930 AN: 2640

East Asian (EAS) AF: 0.988 AC: 3489 AN: 3532

South Asian (SAS) AF: 0.841 AC: 2194 AN: 2610

European-Finnish (FIN) AF: 0.756 AC: 4440 AN: 5870

Middle Eastern (MID) AF: 0.749 AC: 161 AN: 215

European-Non Finnish (NFE) AF: 0.715 AC: 37817 AN: 52882

Other (OTH) AF: 0.823 AC: 1243 AN: 1510

Alfa AF: 0.628 Hom.: 3434

Bravo AF: 0.833

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs798159; hg19: chrX-15900328;