rs1635217

chrX-3302702-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.62 (15285 hom., 20674 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd at 15298 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.623 AC: 69145 AN: 111055 Hom.: 15298 Cov.: 23 AF XY: 0.620 AC XY: 20654 AN XY: 33289

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.639

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: 0.622 AC: 69142 AN: 111111 Hom.: 15285 Cov.: 23 AF XY: 0.620 AC XY: 20674 AN XY: 33355

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.631

Alfa AF: 0.643 Hom.: 6103

Bravo AF: 0.616

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.12
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1635217; hg19: chrX-3220743;