chrX-153052595-T-C

Position:

• chrX-153052595-T-C

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 0.329 in 110,343 control chromosomes in the GnomAD database, including 5,186 homozygotes. There are 10,270 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 0.33 (5186 hom., 10270 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.329 AC: 36255 AN: 110290 Hom.: 5178 Cov.: 22 AF XY: 0.314 AC XY: 10237 AN XY: 32560

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0675

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.329 AC: 36297 AN: 110343 Hom.: 5186 Cov.: 22 AF XY: 0.315 AC XY: 10270 AN XY: 32623

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.327

Alfa AF: 0.256 Hom.: 14659

Bravo AF: 0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6627737; hg19: chrX-152220954;