rs7052082

Positions:

• chrX-745697-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;