chrX-115471502-C-G

Position:

• chrX-115471502-C-G

Variant summary

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

The variant allele was found at a frequency of 0.498 in 110,590 control chromosomes in the GnomAD database, including 11,061 homozygotes. There are 16,660 hemizygotes in GnomAD. 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 0.50 (11061 hom., 16660 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.498 AC: 55048 AN: 110534 Hom.: 11068 Cov.: 23 AF XY: 0.507 AC XY: 16639 AN XY: 32794

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.498 AC: 55058 AN: 110590 Hom.: 11061 Cov.: 23 AF XY: 0.507 AC XY: 16660 AN XY: 32860

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.538

Alfa AF: 0.531 Hom.: 3871

Bravo AF: 0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1883921; hg19: chrX-114706218;