X-42989135-T-C

Variant names:

• chrX-42989135-T-C
• rs1983167

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 0.71 (19867 hom., 22720 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.710 AC: 77839 AN: 109631 Hom.: 19858 Cov.: 22 AF XY: 0.711 AC XY: 22668 AN XY: 31875

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.690

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: 0.710 AC: 77901 AN: 109686 Hom.: 19867 Cov.: 22 AF XY: 0.711 AC XY: 22720 AN XY: 31940

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.693

Alfa AF: 0.693 Hom.: 7503

Bravo AF: 0.718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983167; hg19: chrX-42848384;