rs532649

Positions:

• chrX-67047406-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 0.343 in 110,345 control chromosomes in the GnomAD database, including 8,905 homozygotes. There are 10,484 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 0.34 (8905 hom., 10484 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

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 (AFR) allele frequency at 95% confidence interval = 0.851 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: 0.343 AC: 37779 AN: 110293 Hom.: 8894 Cov.: 22 AF XY: 0.319 AC XY: 10433 AN XY: 32709

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.343 AC: 37846 AN: 110345 Hom.: 8905 Cov.: 22 AF XY: 0.320 AC XY: 10484 AN XY: 32771

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.00143

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.292

Alfa AF: 0.188 Hom.: 4348

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs532649; hg19: chrX-66267248;