rs1202918

chrX-151271258-T-AchrX-151271258-T-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 0.52 (10794 hom., 16312 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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 10789 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: 0.517 AC: 56993 AN: 110304 Hom.: 10789 Cov.: 22 AF XY: 0.500 AC XY: 16283 AN XY: 32572

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.422

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.496

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: 0.517 AC: 57022 AN: 110353 Hom.: 10794 Cov.: 22 AF XY: 0.500 AC XY: 16312 AN XY: 32631

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.500

Alfa AF: 0.497 Hom.: 3557

Bravo AF: 0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.2
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202918; hg19: chrX-150439730;