rs13302591

Variant names:

• chr9-130252358-G-A
• rs13302591

Your query was ambiguous. Multiple possible variants found:

• chr9-130252358-G-A
• chr9-130252358-G-C

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 0.142 in 152,172 control chromosomes in the GnomAD database, including 1,521 homozygotes. 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 0.14 (1521 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.142 AC: 21537 AN: 152054 Hom.: 1517 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.142 AC: 21561 AN: 152172 Hom.: 1521 Cov.: 31 AF XY: 0.139 AC XY: 10337 AN XY: 74384

African (AFR) AF: 0.160 AC: 6633 AN: 41496

American (AMR) AF: 0.125 AC: 1910 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5184

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4818

European-Finnish (FIN) AF: 0.176 AC: 1867 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9491 AN: 68006

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.143 Hom.: 2268

Bravo AF: 0.140

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0030
DANN	Benign	0.62
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13302591; hg19: chr9-133014637;