rs714597

Positions:

• chrX-117862596-T-A
• chrX-117862596-T-C
• chrX-117862596-T-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 0.327 in 108,430 control chromosomes in the GnomAD database, including 4,476 homozygotes. There are 9,963 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 0.33 (4476 hom., 9963 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.327 AC: 35430 AN: 108382 Hom.: 4474 Cov.: 21 AF XY: 0.323 AC XY: 9948 AN XY: 30790

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.387

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.327 AC: 35443 AN: 108430 Hom.: 4476 Cov.: 21 AF XY: 0.323 AC XY: 9963 AN XY: 30848

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.332

Alfa AF: 0.140 Hom.: 661

Bravo AF: 0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714597; hg19: chrX-116996559;