rs17324272

Variant names:

• chrX-133003128-T-C
• rs17324272

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 0.00403 in 109,594 control chromosomes in the GnomAD database, including 13 homozygotes. There are 120 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 0.0040 (13 hom., 120 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00403 AC: 442 AN: 109546 Hom.: 13 Cov.: 21 AF XY: 0.00377 AC XY: 120 AN XY: 31798

Gnomad AFR AF: 0.000898

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00940

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000171

Gnomad OTH AF: 0.00205

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

GnomAD4 genome AF: 0.00403 AC: 442 AN: 109594 Hom.: 13 Cov.: 21 AF XY: 0.00377 AC XY: 120 AN XY: 31856

Gnomad4 AFR AF: 0.000896

Gnomad4 AMR AF: 0.00939

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0876

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000171

Gnomad4 OTH AF: 0.00202

Alfa AF: 0.00108 Hom.: 22

Bravo AF: 0.00610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.016
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17324272; hg19: chrX-132137156;