rs5946326

Variant names:

• chrX-853599-G-A
• rs5946326

Your query was ambiguous. Multiple possible variants found:

• chrX-853599-G-A
• chrX-853599-G-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 0.443 in 151,736 control chromosomes in the GnomAD database, including 15,169 homozygotes. There are 32,910 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 0.44 (15169 hom., 32910 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.443 AC: 67171 AN: 151618 Hom.: 15143 Cov.: 31 AF XY: 0.444 AC XY: 32853 AN XY: 73958

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.443 AC: 67230 AN: 151736 Hom.: 15169 Cov.: 31 AF XY: 0.444 AC XY: 32910 AN XY: 74086

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.491

Bravo AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946326; hg19: chrX-814334;