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).

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: 0.877 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 v4.3

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

Other links and lift over

dbSNP: rs5950584; hg19: chrX-115298204;