rs4829424

Variant names:

• chrX-30303859-A-G
• rs4829424

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 0.2 in 111,712 control chromosomes in the GnomAD database, including 1,616 homozygotes. There are 6,754 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 (1616 hom., 6754 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 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: 0.200 AC: 22318 AN: 111659 Hom.: 1614 Cov.: 23

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.200 AC: 22334 AN: 111712 Hom.: 1616 Cov.: 23 AF XY: 0.199 AC XY: 6754 AN XY: 33878

African (AFR) AF: 0.131 AC: 4047 AN: 30817

American (AMR) AF: 0.276 AC: 2917 AN: 10576

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 523 AN: 2642

East Asian (EAS) AF: 0.237 AC: 839 AN: 3534

South Asian (SAS) AF: 0.199 AC: 527 AN: 2651

European-Finnish (FIN) AF: 0.277 AC: 1659 AN: 5979

Middle Eastern (MID) AF: 0.217 AC: 47 AN: 217

European-Non Finnish (NFE) AF: 0.212 AC: 11260 AN: 53089

Other (OTH) AF: 0.196 AC: 300 AN: 1527

Alfa AF: 0.208 Hom.: 6762

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.45
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs4829424; hg19: chrX-30321976;