rs5941436

chrX-90033228-C-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 0.164 in 108,282 control chromosomes in the GnomAD database, including 1,333 homozygotes. There are 4,940 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 0.16 (1333 hom., 4940 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 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: 0.165 AC: 17816 AN: 108242 Hom.: 1337 Cov.: 22 AF XY: 0.159 AC XY: 4932 AN XY: 30922

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.164 AC: 17811 AN: 108282 Hom.: 1333 Cov.: 22 AF XY: 0.159 AC XY: 4940 AN XY: 30972

Gnomad4 AFR AF: 0.0714

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.164

Alfa AF: 0.205 Hom.: 9151

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	1.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5941436; hg19: chrX-89288227;