rs4827678

Positions:

• chrX-145995800-G-A
• chrX-145995800-G-C

Variant summary

Our verdict is Likely benign. Variant got -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 0.61 (14897 hom., 19231 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.608 AC: 66730 AN: 109735 Hom.: 14889 Cov.: 22 AF XY: 0.599 AC XY: 19191 AN XY: 32049

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.583

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: 0.608 AC: 66773 AN: 109779 Hom.: 14897 Cov.: 22 AF XY: 0.599 AC XY: 19231 AN XY: 32103

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.584

Alfa AF: 0.558 Hom.: 49583

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4827678; hg19: chrX-145077318;