X-50896828-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 0.215 in 112,033 control chromosomes in the GnomAD database, including 2,715 homozygotes. There are 6,911 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 0.21 (2715 hom., 6911 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.214 AC: 24009 AN: 111982 Hom.: 2707 Cov.: 23 AF XY: 0.201 AC XY: 6885 AN XY: 34212

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.215 AC: 24049 AN: 112033 Hom.: 2715 Cov.: 23 AF XY: 0.202 AC XY: 6911 AN XY: 34273

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.198

Alfa AF: 0.0572 Hom.: 278

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.8
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961228; hg19: chrX-50639828;