X-120692753-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 0.65 (16224 hom., 20398 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd at 16223 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: 0.645 AC: 70634 AN: 109480 Hom.: 16223 Cov.: 22 AF XY: 0.640 AC XY: 20351 AN XY: 31790

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.632

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: 0.645 AC: 70679 AN: 109527 Hom.: 16224 Cov.: 22 AF XY: 0.640 AC XY: 20398 AN XY: 31847

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.634

Alfa AF: 0.634 Hom.: 61611

Bravo AF: 0.644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1991961; hg19: chrX-119826608;