X-3492628-A-G

Position:

• chrX-3492628-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;