chrX-136579640-C-T

Variant names:

• chrX-136579640-C-T
• rs2807261

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 (22416 hom., 24653 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.776

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: 0.752 AC: 83432 AN: 110903 Hom.: 22417 Cov.: 23 AF XY: 0.743 AC XY: 24597 AN XY: 33103

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.720

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: 0.752 AC: 83482 AN: 110958 Hom.: 22416 Cov.: 23 AF XY: 0.743 AC XY: 24653 AN XY: 33168

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.725

Alfa AF: 0.690 Hom.: 4250

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2807261; hg19: chrX-135661799;