rs7059886

Variant names:

• chrX-3492628-A-G
• rs7059886

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 0.215 in 110,636 control chromosomes in the GnomAD database, including 2,135 homozygotes. There are 6,858 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 0.21 (2135 hom., 6858 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 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: 0.215 AC: 23747 AN: 110582 Hom.: 2135 Cov.: 22 AF XY: 0.209 AC XY: 6851 AN XY: 32824

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.215 AC: 23753 AN: 110636 Hom.: 2135 Cov.: 22 AF XY: 0.209 AC XY: 6858 AN XY: 32888

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.228

Alfa AF: 0.237 Hom.: 1651

Bravo AF: 0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7059886; hg19: chrX-3410669;