X-30310029-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 0.165 in 110,498 control chromosomes in the GnomAD database, including 1,166 homozygotes. There are 5,217 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 0.17 (1166 hom., 5217 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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: 0.165 AC: 18274 AN: 110446 Hom.: 1165 Cov.: 23 AF XY: 0.159 AC XY: 5206 AN XY: 32692

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.165 AC: 18282 AN: 110498 Hom.: 1166 Cov.: 23 AF XY: 0.159 AC XY: 5217 AN XY: 32754

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.145

Alfa AF: 0.189 Hom.: 5851

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4829169; hg19: chrX-30328146;