rs5923859

Variant names:

• chrX-87172358-A-G
• rs5923859

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 0.56 (12680 hom., 17587 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.556 AC: 61233 AN: 110115 Hom.: 12684 Cov.: 23

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.556

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: 0.556 AC: 61241 AN: 110163 Hom.: 12680 Cov.: 23 AF XY: 0.542 AC XY: 17587 AN XY: 32467

African (AFR) AF: 0.456 AC: 13866 AN: 30380

American (AMR) AF: 0.623 AC: 6410 AN: 10293

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 1621 AN: 2623

East Asian (EAS) AF: 0.179 AC: 625 AN: 3483

South Asian (SAS) AF: 0.387 AC: 1016 AN: 2625

European-Finnish (FIN) AF: 0.565 AC: 3233 AN: 5720

Middle Eastern (MID) AF: 0.710 AC: 152 AN: 214

European-Non Finnish (NFE) AF: 0.626 AC: 32957 AN: 52651

Other (OTH) AF: 0.556 AC: 832 AN: 1497

Alfa AF: 0.598 Hom.: 5131

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5923859;

hg19: chrX-86427361;