chrX-135935372-A-C

Variant names:

• chrX-135935372-A-C
• rs5929706

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 0.98 (37755 hom., 32271 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

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: 0.985 AC: 108851 AN: 110505 Hom.: 37759 Cov.: 23

Gnomad AFR AF: 0.949

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.982

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: 0.985 AC: 108898 AN: 110558 Hom.: 37755 Cov.: 23 AF XY: 0.985 AC XY: 32271 AN XY: 32746

African (AFR) AF: 0.949 AC: 28825 AN: 30366

American (AMR) AF: 0.995 AC: 10291 AN: 10345

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2632 AN: 2633

East Asian (EAS) AF: 1.00 AC: 3508 AN: 3508

South Asian (SAS) AF: 1.00 AC: 2565 AN: 2566

European-Finnish (FIN) AF: 1.00 AC: 5825 AN: 5825

Middle Eastern (MID) AF: 1.00 AC: 216 AN: 216

European-Non Finnish (NFE) AF: 0.999 AC: 52888 AN: 52925

Other (OTH) AF: 0.983 AC: 1469 AN: 1495

Alfa AF: 0.991 Hom.: 10484

Bravo AF: 0.983

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.78
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5929706; hg19: chrX-135017531;