chrX-136078890-A-G

Variant names:

• chrX-136078890-A-G
• rs6528335

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 0.467 in 110,551 control chromosomes in the GnomAD database, including 10,222 homozygotes. There are 14,696 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 0.47 (10222 hom., 14696 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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: 0.466 AC: 51547 AN: 110499 Hom.: 10221 Cov.: 22

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.467 AC: 51583 AN: 110551 Hom.: 10222 Cov.: 22 AF XY: 0.448 AC XY: 14696 AN XY: 32811

African (AFR) AF: 0.764 AC: 23192 AN: 30347

American (AMR) AF: 0.407 AC: 4199 AN: 10323

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 728 AN: 2618

East Asian (EAS) AF: 0.125 AC: 438 AN: 3518

South Asian (SAS) AF: 0.246 AC: 653 AN: 2656

European-Finnish (FIN) AF: 0.381 AC: 2221 AN: 5836

Middle Eastern (MID) AF: 0.350 AC: 75 AN: 214

European-Non Finnish (NFE) AF: 0.364 AC: 19238 AN: 52840

Other (OTH) AF: 0.440 AC: 669 AN: 1519

Alfa AF: 0.410 Hom.: 32092

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.46
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6528335; hg19: chrX-135161049;