rs17267847

Positions:

• chrX-129643057-C-T

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 0.0403 in 112,136 control chromosomes in the GnomAD database, including 86 homozygotes. There are 1,350 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 0.040 (86 hom., 1350 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0404 AC: 4526 AN: 112081 Hom.: 86 Cov.: 24 AF XY: 0.0394 AC XY: 1349 AN XY: 34249

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0166

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.00833

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0403 AC: 4522 AN: 112136 Hom.: 86 Cov.: 24 AF XY: 0.0393 AC XY: 1350 AN XY: 34314

Gnomad4 AFR AF: 0.0253

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0166

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0981

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0392

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0396 Hom.: 317

Bravo AF: 0.0442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17267847; hg19: chrX-128777034;