chrX-83190918-T-G

Position:

• chrX-83190918-T-G

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 0.74 (21949 hom., 24071 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 81081 AN: 109930 Hom.: 21942 Cov.: 22 AF XY: 0.746 AC XY: 24017 AN XY: 32208

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.735

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: 0.738 AC: 81140 AN: 109976 Hom.: 21949 Cov.: 22 AF XY: 0.746 AC XY: 24071 AN XY: 32264

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.738

Alfa AF: 0.614 Hom.: 15528

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs210465; hg19: chrX-82445926;