chrX-891904-T-A

Variant names:

• chrX-891904-T-A
• rs4504827

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 0.394 in 151,514 control chromosomes in the GnomAD database, including 15,247 homozygotes. There are 29,668 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 0.39 (15247 hom., 29668 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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: 0.394 AC: 59594 AN: 151392 Hom.: 15209 Cov.: 31 AF XY: 0.400 AC XY: 29563 AN XY: 73816

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.337

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.394 AC: 59685 AN: 151514 Hom.: 15247 Cov.: 31 AF XY: 0.401 AC XY: 29668 AN XY: 73946

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.359

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.091

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4504827; hg19: chrX-852639;