rs28756697

Variant names:

• chrX-859043-C-T
• rs28756697

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 AF XY: 0.124 AC XY: 9155 AN XY: 74024

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0390

Gnomad4 EAS AF: 0.0893

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0662

Gnomad4 OTH AF: 0.116

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28756697; hg19: chrX-819778;