X-71202153-C-T

Position:

• chrX-71202153-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 0.342 in 110,454 control chromosomes in the GnomAD database, including 5,683 homozygotes. There are 11,173 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 0.34 (5683 hom., 11173 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.342 AC: 37708 AN: 110397 Hom.: 5679 Cov.: 22 AF XY: 0.341 AC XY: 11141 AN XY: 32669

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.342 AC: 37746 AN: 110454 Hom.: 5683 Cov.: 22 AF XY: 0.341 AC XY: 11173 AN XY: 32736

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.330

Alfa AF: 0.288 Hom.: 1855

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525479; hg19: chrX-70422003;