rs5934507

Positions:

• chrX-8949165-A-G
• chrX-8949165-A-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 0.271 in 109,257 control chromosomes in the GnomAD database, including 3,089 homozygotes. There are 8,128 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 0.27 (3089 hom., 8128 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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 (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.271 AC: 29552 AN: 109207 Hom.: 3089 Cov.: 21 AF XY: 0.257 AC XY: 8118 AN XY: 31563

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.271 AC: 29563 AN: 109257 Hom.: 3089 Cov.: 21 AF XY: 0.257 AC XY: 8128 AN XY: 31623

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.279

Alfa AF: 0.274 Hom.: 1687

Bravo AF: 0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5934507; hg19: chrX-8917206;