X-71319639-C-T

Variant names:

• chrX-71319639-C-T
• rs12845815

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 0.75 (21520 hom., 13599 hem., cov: 15)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.754 AC: 69554 AN: 92241 Hom.: 21526 Cov.: 15 AF XY: 0.735 AC XY: 13595 AN XY: 18487

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.788

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: 0.754 AC: 69548 AN: 92249 Hom.: 21520 Cov.: 15 AF XY: 0.735 AC XY: 13599 AN XY: 18505

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.788

Alfa AF: 0.602 Hom.: 1925

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12845815; hg19: chrX-70539489;