rs1977719

Positions:

• chrX-79141646-C-T

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 0.50 (10067 hom., 9398 hem., cov: 16)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.496 AC: 47281 AN: 95328 Hom.: 10073 Cov.: 16 AF XY: 0.435 AC XY: 9393 AN XY: 21612

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.492

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.492

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: 0.496 AC: 47273 AN: 95332 Hom.: 10067 Cov.: 16 AF XY: 0.434 AC XY: 9398 AN XY: 21630

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.492

Alfa AF: 0.545 Hom.: 3512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1977719; hg19: chrX-78397143;