rs5967094

Variant names:

• chrX-100240214-T-C
• rs5967094

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 0.53 (11764 hom., 16838 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

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: 0.533 AC: 58966 AN: 110730 Hom.: 11762 Cov.: 23

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.535

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: 0.533 AC: 59000 AN: 110784 Hom.: 11764 Cov.: 23 AF XY: 0.510 AC XY: 16838 AN XY: 33022

African (AFR) AF: 0.581 AC: 17684 AN: 30429

American (AMR) AF: 0.538 AC: 5610 AN: 10422

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 1525 AN: 2636

East Asian (EAS) AF: 0.167 AC: 588 AN: 3518

South Asian (SAS) AF: 0.260 AC: 689 AN: 2652

European-Finnish (FIN) AF: 0.434 AC: 2554 AN: 5889

Middle Eastern (MID) AF: 0.572 AC: 123 AN: 215

European-Non Finnish (NFE) AF: 0.551 AC: 29130 AN: 52831

Other (OTH) AF: 0.535 AC: 816 AN: 1525

Alfa AF: 0.538 Hom.: 19447

Bravo AF: 0.544

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.72
PhyloP100		0.52

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: rs5967094;

hg19: chrX-99495212;