X-123016678-G-T

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 0.83 (26711 hom., 26596 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 26714 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: 0.826 AC: 90781 AN: 109957 Hom.: 26714 Cov.: 22 AF XY: 0.824 AC XY: 26546 AN XY: 32227

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.907

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.841

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: 0.826 AC: 90822 AN: 110009 Hom.: 26711 Cov.: 22 AF XY: 0.824 AC XY: 26596 AN XY: 32289

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.840

Alfa AF: 0.782 Hom.: 5042

Bravo AF: 0.815

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.8
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1151742; hg19: chrX-122150531;