X-118251602-A-G

Variant names:

• chrX-118251602-A-G
• rs1218117

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 0.55 (12582 hom., 17843 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28
• 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=-0.54).

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: 0.550 AC: 60907 AN: 110723 Hom.: 12590 Cov.: 23

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.551

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: 0.550 AC: 60911 AN: 110779 Hom.: 12582 Cov.: 23 AF XY: 0.541 AC XY: 17843 AN XY: 33005

African (AFR) AF: 0.448 AC: 13665 AN: 30488

American (AMR) AF: 0.347 AC: 3627 AN: 10464

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 1926 AN: 2630

East Asian (EAS) AF: 0.318 AC: 1114 AN: 3503

South Asian (SAS) AF: 0.400 AC: 1054 AN: 2635

European-Finnish (FIN) AF: 0.703 AC: 4089 AN: 5817

Middle Eastern (MID) AF: 0.535 AC: 115 AN: 215

European-Non Finnish (NFE) AF: 0.646 AC: 34127 AN: 52840

Other (OTH) AF: 0.549 AC: 831 AN: 1515

Alfa AF: 0.602 Hom.: 6144

Bravo AF: 0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1218117; hg19: chrX-117385565;