chrX-12865427-C-T

Variant names:

• chrX-12865427-C-T
• rs2897827

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 0.0725 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 8133 AN: 112243 Hom.: 222 Cov.: 24

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

African (AFR) AF: 0.0888 AC: 2744 AN: 30918

American (AMR) AF: 0.0769 AC: 819 AN: 10645

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 141 AN: 2654

East Asian (EAS) AF: 0.0775 AC: 279 AN: 3600

South Asian (SAS) AF: 0.101 AC: 276 AN: 2721

European-Finnish (FIN) AF: 0.0704 AC: 428 AN: 6081

Middle Eastern (MID) AF: 0.0594 AC: 13 AN: 219

European-Non Finnish (NFE) AF: 0.0631 AC: 3359 AN: 53233

Other (OTH) AF: 0.0513 AC: 79 AN: 1540

Alfa AF: 0.0717 Hom.: 552

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
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs2897827; hg19: chrX-12883546;