X-5578052-G-T

Position:

• chrX-5578052-G-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 0.105 in 110,599 control chromosomes in the GnomAD database, including 1,233 homozygotes. There are 3,096 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 0.11 (1233 hom., 3096 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 11643 AN: 110552 Hom.: 1232 Cov.: 23 AF XY: 0.0940 AC XY: 3086 AN XY: 32844

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00534

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.00792

Gnomad FIN AF: 0.00308

Gnomad MID AF: 0.0213

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.105 AC: 11666 AN: 110599 Hom.: 1233 Cov.: 23 AF XY: 0.0941 AC XY: 3096 AN XY: 32901

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.00534

Gnomad4 EAS AF: 0.00142

Gnomad4 SAS AF: 0.00795

Gnomad4 FIN AF: 0.00308

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0454 Hom.: 666

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961738; hg19: chrX-5496093;