X-116166951-G-T

Variant names:

• chrX-116166951-G-T
• rs5950584

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 0.88 (31014 hom., 28993 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• 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=-0.9).

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: 0.877 AC: 96836 AN: 110478 Hom.: 31024 Cov.: 23

Gnomad AFR AF: 0.575

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.907

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: 0.876 AC: 96837 AN: 110528 Hom.: 31014 Cov.: 23 AF XY: 0.883 AC XY: 28993 AN XY: 32846

African (AFR) AF: 0.575 AC: 17488 AN: 30425

American (AMR) AF: 0.950 AC: 9751 AN: 10264

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 2624 AN: 2628

East Asian (EAS) AF: 1.00 AC: 3501 AN: 3501

South Asian (SAS) AF: 0.998 AC: 2564 AN: 2568

European-Finnish (FIN) AF: 1.00 AC: 5915 AN: 5915

Middle Eastern (MID) AF: 0.986 AC: 213 AN: 216

European-Non Finnish (NFE) AF: 0.998 AC: 52741 AN: 52833

Other (OTH) AF: 0.908 AC: 1360 AN: 1498

Alfa AF: 0.899 Hom.: 5924

Bravo AF: 0.858

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		0.33

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: rs5950584;

hg19: chrX-115298204;