rs5912838

chrX-79241621-A-CchrX-79241621-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 0.52 (11058 hom., 16947 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High Homozygotes in GnomAd at 11060 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: 0.522 AC: 57807 AN: 110684 Hom.: 11060 Cov.: 23 AF XY: 0.514 AC XY: 16934 AN XY: 32940

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.530

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: 0.522 AC: 57809 AN: 110736 Hom.: 11058 Cov.: 23 AF XY: 0.514 AC XY: 16947 AN XY: 33002

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.530

Alfa AF: 0.566 Hom.: 37481

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.3
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5912838; hg19: chrX-78497118;