chrX-148161331-T-G

Variant names:

• chrX-148161331-T-G
• rs1990383

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 0.74 (21715 hom., 23462 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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: 0.743 AC: 81311 AN: 109457 Hom.: 21708 Cov.: 22 AF XY: 0.738 AC XY: 23428 AN XY: 31745

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.736

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: 0.743 AC: 81349 AN: 109507 Hom.: 21715 Cov.: 22 AF XY: 0.738 AC XY: 23462 AN XY: 31805

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.721

Gnomad4 OTH AF: 0.738

Alfa AF: 0.727 Hom.: 56064

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1990383; hg19: chrX-147242851;