rs4129148

Variant names:

• chrX-1029445-C-G
• rs4129148

Your query was ambiguous. Multiple possible variants found:

• chrX-1029445-C-G
• chrX-1029445-C-T

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 0.518 in 151,870 control chromosomes in the GnomAD database, including 22,740 homozygotes. There are 38,291 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 0.52 (22740 hom., 38291 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• 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 (NFE) allele frequency at 95% confidence interval = 0.656 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: 0.519 AC: 78706 AN: 151752 Hom.: 22732 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.518 AC: 78725 AN: 151870 Hom.: 22740 Cov.: 31 AF XY: 0.516 AC XY: 38291 AN XY: 74196

African (AFR) AF: 0.252 AC: 10444 AN: 41436

American (AMR) AF: 0.490 AC: 7454 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2163 AN: 3466

East Asian (EAS) AF: 0.429 AC: 2214 AN: 5160

South Asian (SAS) AF: 0.574 AC: 2756 AN: 4804

European-Finnish (FIN) AF: 0.648 AC: 6822 AN: 10528

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.662 AC: 44956 AN: 67956

Other (OTH) AF: 0.552 AC: 1160 AN: 2102

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4129148; hg19: chrX-990180;