X-151981661-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 0.57 (13027 hom., 17774 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd at 13030 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: 0.574 AC: 62443 AN: 108870 Hom.: 13030 Cov.: 21 AF XY: 0.568 AC XY: 17730 AN XY: 31230

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.582

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: 0.574 AC: 62482 AN: 108925 Hom.: 13027 Cov.: 21 AF XY: 0.568 AC XY: 17774 AN XY: 31295

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.583

Alfa AF: 0.559 Hom.: 10703

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981452; hg19: chrX-151150133;