X-858214-A-C

Variant names:

• chrX-858214-A-C
• rs17148729

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 0.298 in 151,716 control chromosomes in the GnomAD database, including 6,997 homozygotes. There are 21,944 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 0.30 (6997 hom., 21944 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• 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 (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.299 AC: 45254 AN: 151596 Hom.: 7005 Cov.: 30

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.298 AC: 45256 AN: 151716 Hom.: 6997 Cov.: 30 AF XY: 0.296 AC XY: 21944 AN XY: 74108

African (AFR) AF: 0.243 AC: 10051 AN: 41404

American (AMR) AF: 0.316 AC: 4800 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3460

East Asian (EAS) AF: 0.342 AC: 1751 AN: 5122

South Asian (SAS) AF: 0.348 AC: 1666 AN: 4788

European-Finnish (FIN) AF: 0.256 AC: 2697 AN: 10544

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22097 AN: 67878

Other (OTH) AF: 0.303 AC: 638 AN: 2108

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.17
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs17148729; hg19: chrX-818949;