rs9306713

chrX-146163912-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;