rs17302090

chrX-67535561-G-A

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 0.0831 in 111,032 control chromosomes in the GnomAD database, including 315 homozygotes. There are 2,476 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 0.083 (315 hom., 2476 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 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: 0.0831 AC: 9219 AN: 110978 Hom.: 315 Cov.: 23 AF XY: 0.0745 AC XY: 2474 AN XY: 33212

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0189

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0621

Gnomad EAS AF: 0.000567

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0818

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0831 AC: 9222 AN: 111032 Hom.: 315 Cov.: 23 AF XY: 0.0744 AC XY: 2476 AN XY: 33276

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0621

Gnomad4 EAS AF: 0.000569

Gnomad4 SAS AF: 0.0231

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0818

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0815 Hom.: 5230

Bravo AF: 0.0854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.55
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17302090; hg19: chrX-66755403;