X-146304706-T-C

Variant names:

• chrX-146304706-T-C
• rs1339482

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 0.427 in 110,918 control chromosomes in the GnomAD database, including 7,373 homozygotes. There are 14,189 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 0.43 (7373 hom., 14189 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 47357 AN: 110858 Hom.: 7368 Cov.: 23

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.427 AC: 47405 AN: 110918 Hom.: 7373 Cov.: 23 AF XY: 0.428 AC XY: 14189 AN XY: 33180

African (AFR) AF: 0.344 AC: 10496 AN: 30554

American (AMR) AF: 0.553 AC: 5779 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1135 AN: 2636

East Asian (EAS) AF: 0.462 AC: 1599 AN: 3462

South Asian (SAS) AF: 0.363 AC: 976 AN: 2689

European-Finnish (FIN) AF: 0.562 AC: 3303 AN: 5878

Middle Eastern (MID) AF: 0.362 AC: 76 AN: 210

European-Non Finnish (NFE) AF: 0.439 AC: 23205 AN: 52854

Other (OTH) AF: 0.445 AC: 673 AN: 1511

Alfa AF: 0.444 Hom.: 34306

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1339482; hg19: chrX-145386224;