X-891904-T-A

Position:

• chrX-891904-T-A

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/exons	MANE	UniProt

Ensembl

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