rs4129664

chrX-25551046-T-C

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 0.12 in 111,592 control chromosomes in the GnomAD database, including 1,810 homozygotes. There are 3,588 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 0.12 (1810 hom., 3588 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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: 0.120 AC: 13339 AN: 111541 Hom.: 1811 Cov.: 22 AF XY: 0.106 AC XY: 3570 AN XY: 33773

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0324

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.0546

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.120 AC: 13355 AN: 111592 Hom.: 1810 Cov.: 22 AF XY: 0.106 AC XY: 3588 AN XY: 33834

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.0477

Gnomad4 ASJ AF: 0.0324

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00710

Gnomad4 FIN AF: 0.00211

Gnomad4 NFE AF: 0.00907

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.0401 Hom.: 725

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129664; hg19: chrX-25569163;