rs5931403

Variant names:

• chrX-138391302-G-A
• rs5931403

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.126 AC: 13996 AN: 111320 Hom.: 643 Cov.: 23

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

African (AFR) AF: 0.0930 AC: 2860 AN: 30746

American (AMR) AF: 0.135 AC: 1411 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 388 AN: 2646

East Asian (EAS) AF: 0.104 AC: 363 AN: 3483

South Asian (SAS) AF: 0.199 AC: 533 AN: 2680

European-Finnish (FIN) AF: 0.151 AC: 900 AN: 5953

Middle Eastern (MID) AF: 0.118 AC: 25 AN: 211

European-Non Finnish (NFE) AF: 0.137 AC: 7259 AN: 52995

Other (OTH) AF: 0.117 AC: 177 AN: 1509

Alfa AF: 0.131 Hom.: 726

Bravo AF: 0.124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.40
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs5931403; hg19: chrX-137473461;