rs7052082

Variant names:

• chrX-745697-C-T
• rs7052082

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 0.0665 in 152,154 control chromosomes in the GnomAD database, including 489 homozygotes. There are 4,794 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 0.067 (489 hom., 4794 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334

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 (NFE) allele frequency at 95% confidence interval = 0.0973 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: 0.0665 AC: 10112 AN: 152036 Hom.: 488 Cov.: 31 AF XY: 0.0644 AC XY: 4783 AN XY: 74252

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0665 AC: 10120 AN: 152154 Hom.: 489 Cov.: 31 AF XY: 0.0645 AC XY: 4794 AN XY: 74380

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.00773

Gnomad4 SAS AF: 0.0509

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.0559

Bravo AF: 0.0589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7052082; hg19: chrX-706432;