rs532649

Variant names:

• chrX-67047406-A-G
• rs532649

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.343 AC: 37779 AN: 110293 Hom.: 8894 Cov.: 22

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

African (AFR) AF: 0.860 AC: 25985 AN: 30232

American (AMR) AF: 0.167 AC: 1731 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 210 AN: 2632

East Asian (EAS) AF: 0.00143 AC: 5 AN: 3501

South Asian (SAS) AF: 0.0723 AC: 191 AN: 2641

European-Finnish (FIN) AF: 0.162 AC: 959 AN: 5909

Middle Eastern (MID) AF: 0.238 AC: 51 AN: 214

European-Non Finnish (NFE) AF: 0.156 AC: 8198 AN: 52666

Other (OTH) AF: 0.292 AC: 438 AN: 1502

Alfa AF: 0.209 Hom.: 9238

Bravo AF: 0.365

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.80
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs532649; hg19: chrX-66267248;