X-71179599-TC-TCC

Variant names:

• chrX-71179599-T-TC
• rs11399763

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (7848 hom., 12298 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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: 0.402 AC: 44288 AN: 110082 Hom.: 7844 Cov.: 0 AF XY: 0.378 AC XY: 12259 AN XY: 32394

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.536

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.403 AC: 44334 AN: 110134 Hom.: 7848 Cov.: 0 AF XY: 0.379 AC XY: 12298 AN XY: 32456

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.423

Asia WGS AF: 0.262 AC: 663 AN: 2522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11399763; hg19: chrX-70399449;