rs9306713

Variant names:

• chrX-146163912-T-C
• rs9306713

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 0.19 in 110,929 control chromosomes in the GnomAD database, including 1,975 homozygotes. There are 5,794 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 0.19 (1975 hom., 5794 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.189 AC: 20980 AN: 110874 Hom.: 1974 Cov.: 22 AF XY: 0.174 AC XY: 5756 AN XY: 33098

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0634

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00705

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.190 AC: 21023 AN: 110929 Hom.: 1975 Cov.: 22 AF XY: 0.175 AC XY: 5794 AN XY: 33163

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00707

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.178

Alfa AF: 0.146 Hom.: 5979

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
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: rs9306713; hg19: chrX-145245430;