chrX-66117875-G-T

Variant names:

• chrX-66117875-G-T
• rs1359524

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 0.73 (22070 hom., 24232 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• 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=-0.92).

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: 0.726 AC: 80411 AN: 110721 Hom.: 22076 Cov.: 23

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.855

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.771

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: 0.726 AC: 80419 AN: 110775 Hom.: 22070 Cov.: 23 AF XY: 0.734 AC XY: 24232 AN XY: 33025

African (AFR) AF: 0.390 AC: 11897 AN: 30510

American (AMR) AF: 0.799 AC: 8269 AN: 10352

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2142 AN: 2631

East Asian (EAS) AF: 0.999 AC: 3529 AN: 3534

South Asian (SAS) AF: 0.903 AC: 2351 AN: 2603

European-Finnish (FIN) AF: 0.864 AC: 5012 AN: 5804

Middle Eastern (MID) AF: 0.845 AC: 180 AN: 213

European-Non Finnish (NFE) AF: 0.855 AC: 45280 AN: 52936

Other (OTH) AF: 0.772 AC: 1166 AN: 1511

Alfa AF: 0.761 Hom.: 8390

Bravo AF: 0.710

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.61
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1359524; hg19: chrX-65337717;