chrX-71212113-A-C

Variant names:

• chrX-71212113-A-C
• rs7058793

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.37 (7386 hom., 9759 hem., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

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: 0.369 AC: 38960 AN: 105472 Hom.: 7381 Cov.: 19 AF XY: 0.340 AC XY: 9746 AN XY: 28638

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.370 AC: 38981 AN: 105492 Hom.: 7386 Cov.: 19 AF XY: 0.340 AC XY: 9759 AN XY: 28670

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.337

Alfa AF: 0.265 Hom.: 12714

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7058793; hg19: chrX-70431963;