rs5905613

Variant names:

• chrX-43648052-T-C
• rs5905613

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 0.62 (15855 hom., 19845 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• 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=-0.91).

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: 0.623 AC: 68496 AN: 109948 Hom.: 15855 Cov.: 22

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.657

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: 0.623 AC: 68526 AN: 110007 Hom.: 15855 Cov.: 22 AF XY: 0.615 AC XY: 19845 AN XY: 32287

African (AFR) AF: 0.447 AC: 13520 AN: 30217

American (AMR) AF: 0.796 AC: 8169 AN: 10268

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 1809 AN: 2608

East Asian (EAS) AF: 0.528 AC: 1822 AN: 3449

South Asian (SAS) AF: 0.429 AC: 1124 AN: 2620

European-Finnish (FIN) AF: 0.564 AC: 3252 AN: 5764

Middle Eastern (MID) AF: 0.704 AC: 152 AN: 216

European-Non Finnish (NFE) AF: 0.707 AC: 37247 AN: 52693

Other (OTH) AF: 0.656 AC: 987 AN: 1504

Alfa AF: 0.679 Hom.: 83771

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		0.39

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: rs5905613;

hg19: chrX-43507300;