X-66529354-C-T

Variant names:

• chrX-66529354-C-T
• rs1158928

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 0.71 (20712 hom., 23310 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.713 AC: 78358 AN: 109892 Hom.: 20715 Cov.: 22

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.753

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: 0.713 AC: 78369 AN: 109943 Hom.: 20712 Cov.: 22 AF XY: 0.722 AC XY: 23310 AN XY: 32271

African (AFR) AF: 0.442 AC: 13399 AN: 30316

American (AMR) AF: 0.858 AC: 8848 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2401 AN: 2612

East Asian (EAS) AF: 0.997 AC: 3500 AN: 3511

South Asian (SAS) AF: 0.901 AC: 2315 AN: 2568

European-Finnish (FIN) AF: 0.752 AC: 4313 AN: 5739

Middle Eastern (MID) AF: 0.805 AC: 169 AN: 210

European-Non Finnish (NFE) AF: 0.794 AC: 41689 AN: 52492

Other (OTH) AF: 0.756 AC: 1137 AN: 1503

Alfa AF: 0.659 Hom.: 9207

Bravo AF: 0.711

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1158928; hg19: chrX-65749196;