X-858939-T-A

Variant names:

• chrX-858939-T-A
• 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 0.203 in 151,850 control chromosomes in the GnomAD database, including 3,406 homozygotes. There are 14,757 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 0.20 (3406 hom., 14757 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.203 AC: 30828 AN: 151732 Hom.: 3394 Cov.: 31

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.203 AC: 30877 AN: 151850 Hom.: 3406 Cov.: 31 AF XY: 0.199 AC XY: 14757 AN XY: 74202

African (AFR) AF: 0.281 AC: 11622 AN: 41398

American (AMR) AF: 0.128 AC: 1957 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3464

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5156

South Asian (SAS) AF: 0.208 AC: 1000 AN: 4804

European-Finnish (FIN) AF: 0.141 AC: 1487 AN: 10572

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12789 AN: 67912

Other (OTH) AF: 0.176 AC: 371 AN: 2106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.10
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;