rs3131302

Variant names:

• chrX-51568002-T-C
• rs3131302

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 0.148 in 111,048 control chromosomes in the GnomAD database, including 1,165 homozygotes. There are 4,825 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 0.15 (1165 hom., 4825 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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: 0.148 AC: 16401 AN: 110994 Hom.: 1164 Cov.: 23

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.148 AC: 16405 AN: 111048 Hom.: 1165 Cov.: 23 AF XY: 0.145 AC XY: 4825 AN XY: 33242

African (AFR) AF: 0.0346 AC: 1064 AN: 30734

American (AMR) AF: 0.121 AC: 1257 AN: 10366

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 288 AN: 2640

East Asian (EAS) AF: 0.0396 AC: 140 AN: 3531

South Asian (SAS) AF: 0.177 AC: 464 AN: 2617

European-Finnish (FIN) AF: 0.253 AC: 1471 AN: 5804

Middle Eastern (MID) AF: 0.157 AC: 34 AN: 217

European-Non Finnish (NFE) AF: 0.213 AC: 11267 AN: 52948

Other (OTH) AF: 0.140 AC: 212 AN: 1513

Alfa AF: 0.199 Hom.: 3217

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.49
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs3131302; hg19: chrX-51310854;