X-129970758-A-G

Variant names:

• chrX-129970758-A-G
• rs2361405

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 0.271 in 108,788 control chromosomes in the GnomAD database, including 4,662 homozygotes. There are 8,305 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 0.27 (4662 hom., 8305 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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: 0.271 AC: 29469 AN: 108742 Hom.: 4653 Cov.: 22

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.271 AC: 29521 AN: 108788 Hom.: 4662 Cov.: 22 AF XY: 0.265 AC XY: 8305 AN XY: 31300

African (AFR) AF: 0.547 AC: 16302 AN: 29789

American (AMR) AF: 0.289 AC: 2907 AN: 10061

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 462 AN: 2613

East Asian (EAS) AF: 0.692 AC: 2375 AN: 3434

South Asian (SAS) AF: 0.314 AC: 803 AN: 2554

European-Finnish (FIN) AF: 0.122 AC: 673 AN: 5539

Middle Eastern (MID) AF: 0.214 AC: 45 AN: 210

European-Non Finnish (NFE) AF: 0.103 AC: 5426 AN: 52456

Other (OTH) AF: 0.300 AC: 441 AN: 1469

Alfa AF: 0.0570 Hom.: 260

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.56
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2361405; hg19: chrX-129104734;