rs4830187

Variant names:

• chrX-130378769-C-T
• rs4830187

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 0.343 in 109,079 control chromosomes in the GnomAD database, including 5,180 homozygotes. There are 10,777 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 0.34 (5180 hom., 10777 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 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: 0.344 AC: 37468 AN: 109030 Hom.: 5186 Cov.: 21

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.343 AC: 37456 AN: 109079 Hom.: 5180 Cov.: 21 AF XY: 0.342 AC XY: 10777 AN XY: 31475

African (AFR) AF: 0.155 AC: 4660 AN: 30049

American (AMR) AF: 0.340 AC: 3454 AN: 10163

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1067 AN: 2630

East Asian (EAS) AF: 0.350 AC: 1206 AN: 3441

South Asian (SAS) AF: 0.420 AC: 1053 AN: 2510

European-Finnish (FIN) AF: 0.341 AC: 1893 AN: 5547

Middle Eastern (MID) AF: 0.410 AC: 86 AN: 210

European-Non Finnish (NFE) AF: 0.445 AC: 23306 AN: 52383

Other (OTH) AF: 0.336 AC: 497 AN: 1479

Alfa AF: 0.400 Hom.: 23759

Bravo AF: 0.333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.67
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs4830187; hg19: chrX-129512743;