X-86937000-G-T

Variant names:

• chrX-86937000-G-T
• rs2710057

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 0.72 (20504 hom., 23064 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

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: 0.721 AC: 79308 AN: 109926 Hom.: 20506 Cov.: 22 AF XY: 0.715 AC XY: 23003 AN XY: 32190

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.734

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: 0.722 AC: 79359 AN: 109980 Hom.: 20504 Cov.: 22 AF XY: 0.715 AC XY: 23064 AN XY: 32254

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.732

Alfa AF: 0.708 Hom.: 83134

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2710057; hg19: chrX-86192003;