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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;