X-51483638-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 0.66 (17026 hom., 21741 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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 17027 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: 0.659 AC: 72880 AN: 110665 Hom.: 17027 Cov.: 24 AF XY: 0.660 AC XY: 21713 AN XY: 32911

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.675

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: 0.658 AC: 72904 AN: 110719 Hom.: 17026 Cov.: 24 AF XY: 0.659 AC XY: 21741 AN XY: 32975

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.679

Alfa AF: 0.645 Hom.: 6112

Bravo AF: 0.675

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.4
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5987421; hg19: chrX-51226490;