chrX-117247696-T-C

Position:

• chrX-117247696-T-C

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 0.458 in 111,355 control chromosomes in the GnomAD database, including 8,610 homozygotes. There are 15,124 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 0.46 (8610 hom., 15124 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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: 0.458 AC: 50956 AN: 111301 Hom.: 8615 Cov.: 24 AF XY: 0.450 AC XY: 15104 AN XY: 33597

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.457

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.458 AC: 50967 AN: 111355 Hom.: 8610 Cov.: 24 AF XY: 0.449 AC XY: 15124 AN XY: 33661

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.445

Alfa AF: 0.488 Hom.: 2679

Bravo AF: 0.438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.48
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs886605; hg19: chrX-116381659;