X-35047456-G-A

Variant names:

• chrX-35047456-G-A
• rs5928719

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 0.179 in 111,139 control chromosomes in the GnomAD database, including 1,293 homozygotes. There are 5,660 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 0.18 (1293 hom., 5660 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 19917 AN: 111086 Hom.: 1294 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.179 AC: 19927 AN: 111139 Hom.: 1293 Cov.: 22 AF XY: 0.169 AC XY: 5660 AN XY: 33395

African (AFR) AF: 0.218 AC: 6655 AN: 30489

American (AMR) AF: 0.140 AC: 1471 AN: 10477

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 463 AN: 2643

East Asian (EAS) AF: 0.139 AC: 490 AN: 3515

South Asian (SAS) AF: 0.174 AC: 462 AN: 2656

European-Finnish (FIN) AF: 0.163 AC: 971 AN: 5943

Middle Eastern (MID) AF: 0.134 AC: 29 AN: 217

European-Non Finnish (NFE) AF: 0.170 AC: 9030 AN: 52999

Other (OTH) AF: 0.150 AC: 227 AN: 1515

Alfa AF: 0.173 Hom.: 2879

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs5928719; hg19: chrX-35065573;