rs6521896

Variant names:

• chrX-50901769-A-G
• rs6521896

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 0.218 in 110,975 control chromosomes in the GnomAD database, including 2,828 homozygotes. There are 6,794 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 0.22 (2828 hom., 6794 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 3 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 = 0.451 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: 0.218 AC: 24127 AN: 110922 Hom.: 2819 Cov.: 22

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.218 AC: 24171 AN: 110975 Hom.: 2828 Cov.: 22 AF XY: 0.205 AC XY: 6794 AN XY: 33217

African (AFR) AF: 0.458 AC: 13891 AN: 30359

American (AMR) AF: 0.130 AC: 1368 AN: 10489

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 282 AN: 2636

East Asian (EAS) AF: 0.0378 AC: 133 AN: 3522

South Asian (SAS) AF: 0.174 AC: 451 AN: 2595

European-Finnish (FIN) AF: 0.110 AC: 653 AN: 5914

Middle Eastern (MID) AF: 0.187 AC: 40 AN: 214

European-Non Finnish (NFE) AF: 0.131 AC: 6952 AN: 53040

Other (OTH) AF: 0.206 AC: 314 AN: 1523

Alfa AF: 0.192 Hom.: 1870

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.60
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs6521896; hg19: chrX-50644769;