rs5946526

Variant names:

• chrX-877619-C-G
• rs5946526

Your query was ambiguous. Multiple possible variants found:

• chrX-877619-C-G
• chrX-877619-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 0.317 in 151,980 control chromosomes in the GnomAD database, including 8,089 homozygotes. There are 23,705 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 0.32 (8089 hom., 23705 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.316 AC: 48054 AN: 151862 Hom.: 8066 Cov.: 32 AF XY: 0.319 AC XY: 23650 AN XY: 74130

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.317 AC: 48117 AN: 151980 Hom.: 8089 Cov.: 32 AF XY: 0.319 AC XY: 23705 AN XY: 74258

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.311

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946526; hg19: chrX-838354;