rs5980075

Variant names:

• chrX-14932409-A-G
• rs5980075

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 0.63 (15959 hom., 19763 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• 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=-0.95).

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: 0.626 AC: 68883 AN: 110004 Hom.: 15967 Cov.: 22

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.593

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: 0.626 AC: 68910 AN: 110056 Hom.: 15959 Cov.: 22 AF XY: 0.611 AC XY: 19763 AN XY: 32342

African (AFR) AF: 0.733 AC: 22104 AN: 30159

American (AMR) AF: 0.530 AC: 5479 AN: 10339

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1469 AN: 2626

East Asian (EAS) AF: 0.185 AC: 645 AN: 3495

South Asian (SAS) AF: 0.410 AC: 1052 AN: 2564

European-Finnish (FIN) AF: 0.626 AC: 3610 AN: 5771

Middle Eastern (MID) AF: 0.588 AC: 127 AN: 216

European-Non Finnish (NFE) AF: 0.625 AC: 32952 AN: 52719

Other (OTH) AF: 0.589 AC: 879 AN: 1492

Alfa AF: 0.620 Hom.: 23951

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.81
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs5980075; hg19: chrX-14950531;