rs7052082

Variant names:

• chrX-745697-C-T
• rs7052082

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10112 AN: 152036 Hom.: 488 Cov.: 31

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

African (AFR) AF: 0.0217 AC: 900 AN: 41542

American (AMR) AF: 0.0549 AC: 839 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3470

East Asian (EAS) AF: 0.00773 AC: 40 AN: 5174

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4814

European-Finnish (FIN) AF: 0.0954 AC: 1009 AN: 10580

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6751 AN: 67976

Other (OTH) AF: 0.0559 AC: 118 AN: 2110

Bravo AF: 0.0589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs7052082; hg19: chrX-706432;