rs28756697

Positions:

• chrX-859043-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;