rs4825172

Variant names:

• chrX-143673326-C-T
• rs4825172

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 0.303 in 110,037 control chromosomes in the GnomAD database, including 3,863 homozygotes. There are 9,787 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 (3863 hom., 9787 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.303 AC: 33278 AN: 109994 Hom.: 3855 Cov.: 22

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.303 AC: 33294 AN: 110037 Hom.: 3863 Cov.: 22 AF XY: 0.303 AC XY: 9787 AN XY: 32337

African (AFR) AF: 0.167 AC: 5082 AN: 30394

American (AMR) AF: 0.375 AC: 3835 AN: 10229

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 936 AN: 2630

East Asian (EAS) AF: 0.346 AC: 1204 AN: 3476

South Asian (SAS) AF: 0.492 AC: 1272 AN: 2587

European-Finnish (FIN) AF: 0.318 AC: 1790 AN: 5630

Middle Eastern (MID) AF: 0.344 AC: 73 AN: 212

European-Non Finnish (NFE) AF: 0.350 AC: 18463 AN: 52722

Other (OTH) AF: 0.326 AC: 485 AN: 1488

Alfa AF: 0.318 Hom.: 13406

Bravo AF: 0.295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4825172; hg19: chrX-142756404;