chrX-98263070-G-A

Variant names:

• chrX-98263070-G-A
• rs915336

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 0.72 (20128 hom., 24208 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• 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=-0.99).

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: 0.715 AC: 79393 AN: 111029 Hom.: 20131 Cov.: 24

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.770

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.737

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: 0.715 AC: 79429 AN: 111078 Hom.: 20128 Cov.: 24 AF XY: 0.727 AC XY: 24208 AN XY: 33320

African (AFR) AF: 0.545 AC: 16627 AN: 30534

American (AMR) AF: 0.784 AC: 8220 AN: 10486

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 1955 AN: 2642

East Asian (EAS) AF: 0.901 AC: 3160 AN: 3509

South Asian (SAS) AF: 0.810 AC: 2161 AN: 2669

European-Finnish (FIN) AF: 0.835 AC: 4916 AN: 5890

Middle Eastern (MID) AF: 0.750 AC: 159 AN: 212

European-Non Finnish (NFE) AF: 0.765 AC: 40478 AN: 52936

Other (OTH) AF: 0.733 AC: 1114 AN: 1519

Alfa AF: 0.749 Hom.: 6166

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.75
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs915336; hg19: chrX-97518068;