rs321029

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).

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: 0.781 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 v4.3

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;