rs2897827

chrX-12865427-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 0.0725 in 112,296 control chromosomes in the GnomAD database, including 222 homozygotes. There are 2,550 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 0.072 (222 hom., 2550 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0916 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: 0.0725 AC: 8133 AN: 112243 Hom.: 222 Cov.: 24 AF XY: 0.0738 AC XY: 2542 AN XY: 34463

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.0667

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0519

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

GnomAD4 genome AF: 0.0725 AC: 8139 AN: 112296 Hom.: 222 Cov.: 24 AF XY: 0.0739 AC XY: 2550 AN XY: 34526

Gnomad4 AFR AF: 0.0888

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.0775

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.0631

Gnomad4 OTH AF: 0.0513

Alfa AF: 0.0740 Hom.: 512

Bravo AF: 0.0743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2897827; hg19: chrX-12883546;