X-78328249-A-G

Variant names:

• chrX-78328249-A-G
• rs321029

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 0.78 (24349 hom., 24253 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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: 0.781 AC: 85329 AN: 109229 Hom.: 24357 Cov.: 21

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.754

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: 0.781 AC: 85368 AN: 109286 Hom.: 24349 Cov.: 21 AF XY: 0.769 AC XY: 24253 AN XY: 31556

African (AFR) AF: 0.889 AC: 26645 AN: 29974

American (AMR) AF: 0.666 AC: 6804 AN: 10211

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2134 AN: 2617

East Asian (EAS) AF: 0.588 AC: 2029 AN: 3450

South Asian (SAS) AF: 0.610 AC: 1537 AN: 2519

European-Finnish (FIN) AF: 0.770 AC: 4344 AN: 5640

Middle Eastern (MID) AF: 0.759 AC: 161 AN: 212

European-Non Finnish (NFE) AF: 0.765 AC: 40155 AN: 52510

Other (OTH) AF: 0.751 AC: 1113 AN: 1483

Alfa AF: 0.823 Hom.: 13439

Bravo AF: 0.779

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.6
DANN	Benign	0.85
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs321029; hg19: chrX-77583746;