rs4129148

chrX-1029445-C-GchrX-1029445-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78706 AN: 151752 Hom.: 22732 Cov.: 31 AF XY: 0.517 AC XY: 38266 AN XY: 74068

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

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.552

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129148; hg19: chrX-990180;