rs1474563

chrX-79393696-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 0.469 in 109,788 control chromosomes in the GnomAD database, including 9,376 homozygotes. There are 15,136 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 0.47 (9376 hom., 15136 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 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: 0.469 AC: 51503 AN: 109732 Hom.: 9379 Cov.: 22 AF XY: 0.472 AC XY: 15112 AN XY: 32020

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.469 AC: 51524 AN: 109788 Hom.: 9376 Cov.: 22 AF XY: 0.472 AC XY: 15136 AN XY: 32086

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.505

Alfa AF: 0.555 Hom.: 59549

Bravo AF: 0.446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.1
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1474563; hg19: chrX-78649193;