rs17051551

Variant names:

• chrX-3224334-T-C
• rs17051551

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 0.25 in 110,565 control chromosomes in the GnomAD database, including 2,538 homozygotes. There are 8,057 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 0.25 (2538 hom., 8057 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 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: 0.250 AC: 27611 AN: 110511 Hom.: 2543 Cov.: 22 AF XY: 0.245 AC XY: 8039 AN XY: 32775

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.243

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.250 AC: 27617 AN: 110565 Hom.: 2538 Cov.: 22 AF XY: 0.245 AC XY: 8057 AN XY: 32839

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.245

Alfa AF: 0.243 Hom.: 19333

Bravo AF: 0.245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17051551; hg19: chrX-3142375;