rs5987724

Variant names:

• chrX-103324188-A-C
• rs5987724

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 0.67 (18715 hom., 21519 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.671 AC: 73953 AN: 110211 Hom.: 18712 Cov.: 23

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.642

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: 0.671 AC: 74006 AN: 110264 Hom.: 18715 Cov.: 23 AF XY: 0.662 AC XY: 21519 AN XY: 32516

African (AFR) AF: 0.911 AC: 27656 AN: 30361

American (AMR) AF: 0.619 AC: 6420 AN: 10374

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 1756 AN: 2625

East Asian (EAS) AF: 0.599 AC: 2083 AN: 3479

South Asian (SAS) AF: 0.742 AC: 1889 AN: 2545

European-Finnish (FIN) AF: 0.470 AC: 2699 AN: 5743

Middle Eastern (MID) AF: 0.545 AC: 116 AN: 213

European-Non Finnish (NFE) AF: 0.572 AC: 30166 AN: 52730

Other (OTH) AF: 0.642 AC: 974 AN: 1516

Alfa AF: 0.617 Hom.: 4846

Bravo AF: 0.691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.54
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs5987724; hg19: chrX-102579116;