X-81007519-T-C

Variant names:

• chrX-81007519-T-C
• rs1166638

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 0.65 (17672 hom., 21454 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.649 AC: 71737 AN: 110550 Hom.: 17681 Cov.: 23 AF XY: 0.653 AC XY: 21411 AN XY: 32796

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.779

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.654

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: 0.649 AC: 71761 AN: 110602 Hom.: 17672 Cov.: 23 AF XY: 0.653 AC XY: 21454 AN XY: 32858

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.656

Alfa AF: 0.682 Hom.: 4460

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1166638; hg19: chrX-80263018;