rs714597

Variant names:

• chrX-117862596-T-A
• rs714597

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;