X-84961903-A-G

Variant names:

• chrX-84961903-A-G
• rs4828313

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 0.74 (21155 hom., 24085 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• 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=-0.92).

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: 0.737 AC: 81118 AN: 110027 Hom.: 21158 Cov.: 22

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.749

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: 0.737 AC: 81165 AN: 110079 Hom.: 21155 Cov.: 22 AF XY: 0.744 AC XY: 24085 AN XY: 32373

African (AFR) AF: 0.831 AC: 25241 AN: 30389

American (AMR) AF: 0.733 AC: 7536 AN: 10281

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 1993 AN: 2626

East Asian (EAS) AF: 0.676 AC: 2342 AN: 3466

South Asian (SAS) AF: 0.855 AC: 2221 AN: 2597

European-Finnish (FIN) AF: 0.739 AC: 4265 AN: 5769

Middle Eastern (MID) AF: 0.812 AC: 173 AN: 213

European-Non Finnish (NFE) AF: 0.683 AC: 35885 AN: 52576

Other (OTH) AF: 0.748 AC: 1118 AN: 1495

Alfa AF: 0.709 Hom.: 5712

Bravo AF: 0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs4828313; hg19: chrX-84216909; COSMIC: COSV53902959;