X-51467205-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 0.29 in 110,990 control chromosomes in the GnomAD database, including 3,632 homozygotes. There are 9,390 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 0.29 (3632 hom., 9390 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.290 AC: 32135 AN: 110935 Hom.: 3635 Cov.: 23 AF XY: 0.282 AC XY: 9380 AN XY: 33207

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.290 AC: 32133 AN: 110990 Hom.: 3632 Cov.: 23 AF XY: 0.282 AC XY: 9390 AN XY: 33272

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.272

Alfa AF: 0.341 Hom.: 24816

Bravo AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	4.6
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327301; hg19: chrX-51210057;