rs17148729

Variant names:

• chrX-858214-A-C
• rs17148729

Your query was ambiguous. Multiple possible variants found:

• chrX-858214-A-C
• chrX-858214-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 0.298 in 151,716 control chromosomes in the GnomAD database, including 6,997 homozygotes. There are 21,944 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 0.30 (6997 hom., 21944 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.299 AC: 45254 AN: 151596 Hom.: 7005 Cov.: 30 AF XY: 0.296 AC XY: 21932 AN XY: 73980

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.298 AC: 45256 AN: 151716 Hom.: 6997 Cov.: 30 AF XY: 0.296 AC XY: 21944 AN XY: 74108

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.303

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17148729; hg19: chrX-818949;