rs825541

Variant names:

• chrX-83794840-G-A
• rs825541

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;