chrX-25739567-G-T

Variant names:

• chrX-25739567-G-T
• rs12688703

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 0.352 in 110,493 control chromosomes in the GnomAD database, including 5,121 homozygotes. There are 11,621 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 0.35 (5121 hom., 11621 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.352 AC: 38848 AN: 110441 Hom.: 5123 Cov.: 23

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0940

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.352 AC: 38851 AN: 110493 Hom.: 5121 Cov.: 23 AF XY: 0.354 AC XY: 11621 AN XY: 32801

African (AFR) AF: 0.246 AC: 7497 AN: 30491

American (AMR) AF: 0.432 AC: 4464 AN: 10339

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 997 AN: 2619

East Asian (EAS) AF: 0.630 AC: 2181 AN: 3460

South Asian (SAS) AF: 0.423 AC: 1104 AN: 2608

European-Finnish (FIN) AF: 0.448 AC: 2593 AN: 5790

Middle Eastern (MID) AF: 0.258 AC: 55 AN: 213

European-Non Finnish (NFE) AF: 0.367 AC: 19351 AN: 52776

Other (OTH) AF: 0.359 AC: 545 AN: 1516

Alfa AF: 0.241 Hom.: 1514

Bravo AF: 0.357

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0020
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12688703; hg19: chrX-25757684;