rs28756697

Variant names:

• chrX-859043-C-T
• rs28756697

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 0.124 in 151,772 control chromosomes in the GnomAD database, including 1,686 homozygotes. There are 9,207 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 0.12 (1686 hom., 9207 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18693 AN: 151656 Hom.: 1668 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0390

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.124 AC: 18768 AN: 151772 Hom.: 1686 Cov.: 31 AF XY: 0.124 AC XY: 9207 AN XY: 74150

African (AFR) AF: 0.243 AC: 10038 AN: 41352

American (AMR) AF: 0.151 AC: 2293 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0390 AC: 135 AN: 3464

East Asian (EAS) AF: 0.0893 AC: 459 AN: 5142

South Asian (SAS) AF: 0.130 AC: 625 AN: 4812

European-Finnish (FIN) AF: 0.0404 AC: 426 AN: 10538

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0662 AC: 4495 AN: 67930

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Bravo AF: 0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs28756697; hg19: chrX-819778;