rs915336

chrX-98263070-G-AchrX-98263070-G-C

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 0.72 (20128 hom., 24208 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd at 20131 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: 0.715 AC: 79393 AN: 111029 Hom.: 20131 Cov.: 24 AF XY: 0.726 AC XY: 24163 AN XY: 33261

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.770

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.737

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: 0.715 AC: 79429 AN: 111078 Hom.: 20128 Cov.: 24 AF XY: 0.727 AC XY: 24208 AN XY: 33320

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.733

Alfa AF: 0.749 Hom.: 6166

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	4.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs915336; hg19: chrX-97518068;