rs825541

Positions:

• chrX-83794840-G-A

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 0.121 in 111,332 control chromosomes in the GnomAD database, including 785 homozygotes. There are 3,973 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 (785 hom., 3973 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.121 AC: 13443 AN: 111280 Hom.: 788 Cov.: 23 AF XY: 0.119 AC XY: 3970 AN XY: 33484

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.0959

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.121 AC: 13440 AN: 111332 Hom.: 785 Cov.: 23 AF XY: 0.118 AC XY: 3973 AN XY: 33546

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.105

Alfa AF: 0.116 Hom.: 5890

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
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: rs825541; hg19: chrX-83049848;