X-858939-T-C

Variant names:

• chrX-858939-T-C
• rs35352127

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 0.0326 in 151,926 control chromosomes in the GnomAD database, including 184 homozygotes. There are 2,600 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 0.033 (184 hom., 2600 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0991 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: 0.0324 AC: 4918 AN: 151806 Hom.: 174 Cov.: 31

Gnomad AFR AF: 0.0115

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0830

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0326 AC: 4957 AN: 151926 Hom.: 184 Cov.: 31 AF XY: 0.0350 AC XY: 2600 AN XY: 74258

African (AFR) AF: 0.0114 AC: 474 AN: 41432

American (AMR) AF: 0.103 AC: 1574 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3464

East Asian (EAS) AF: 0.0834 AC: 430 AN: 5158

South Asian (SAS) AF: 0.0730 AC: 351 AN: 4808

European-Finnish (FIN) AF: 0.0107 AC: 113 AN: 10584

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0273 AC: 1857 AN: 67936

Other (OTH) AF: 0.0417 AC: 88 AN: 2110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.15
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs35352127; hg19: chrX-819674;