X-143204188-A-G

Variant names:

• chrX-143204188-A-G
• rs10521838

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 0.202 in 110,354 control chromosomes in the GnomAD database, including 1,840 homozygotes. There are 6,471 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 (1840 hom., 6471 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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: 0.202 AC: 22317 AN: 110305 Hom.: 1839 Cov.: 23

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.202 AC: 22331 AN: 110354 Hom.: 1840 Cov.: 23 AF XY: 0.197 AC XY: 6471 AN XY: 32806

African (AFR) AF: 0.309 AC: 9344 AN: 30260

American (AMR) AF: 0.119 AC: 1242 AN: 10403

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 361 AN: 2639

East Asian (EAS) AF: 0.0465 AC: 163 AN: 3502

South Asian (SAS) AF: 0.119 AC: 316 AN: 2664

European-Finnish (FIN) AF: 0.262 AC: 1523 AN: 5813

Middle Eastern (MID) AF: 0.187 AC: 39 AN: 209

European-Non Finnish (NFE) AF: 0.170 AC: 8967 AN: 52672

Other (OTH) AF: 0.180 AC: 272 AN: 1513

Alfa AF: 0.179 Hom.: 12333

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.75
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10521838; hg19: chrX-142291974;