rs5931403

chrX-138391302-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 0.126 in 111,369 control chromosomes in the GnomAD database, including 648 homozygotes. There are 4,099 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 0.13 (648 hom., 4099 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.126 AC: 13996 AN: 111320 Hom.: 643 Cov.: 23 AF XY: 0.122 AC XY: 4093 AN XY: 33562

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.126 AC: 14011 AN: 111369 Hom.: 648 Cov.: 23 AF XY: 0.122 AC XY: 4099 AN XY: 33621

Gnomad4 AFR AF: 0.0930

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.117

Alfa AF: 0.131 Hom.: 726

Bravo AF: 0.124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.39
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5931403; hg19: chrX-137473461;