X-143204188-A-G

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 0.202 in 110,354 control chromosomes in the GnomAD database, including 1,840 homozygotes. There are 6,471 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 0.20 (1840 hom., 6471 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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: 0.202 AC: 22317 AN: 110305 Hom.: 1839 Cov.: 23 AF XY: 0.197 AC XY: 6461 AN XY: 32747

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.202 AC: 22331 AN: 110354 Hom.: 1840 Cov.: 23 AF XY: 0.197 AC XY: 6471 AN XY: 32806

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.180

Alfa AF: 0.166 Hom.: 8277

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521838; hg19: chrX-142291974;