X-71179599-TC-TCC

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;